Process for preparation of tacrolimus

- Lek Pharmaceuticals D.D.

Genetically modified strains of Streptomyces tsukubaensis (S. tsukubaensis) can be used for an improved fermentation process for the preparation of tacrolimus or a salt or derivative thereof by cultivation of these genetically modified strains. Novel genes allowing biosynthesis of allylmalonyl-CoA can be used for polyketide production with allylmalonyl extender unit.

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Description
CROSS-REFERENCE TO RELATED APPLICATION

This application is a National Stage entry of International Application No. PCT/EP2010/059896, filed Jul. 9, 2010, which claims priority to European Application No. 09165035.8, filed Jul. 9, 2009, the entire specifications, claims and drawings of which are incorporated herewith by reference.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jun. 7, 2012, is named 02948900.txt and is 74,907 bytes in size.

The present invention relates to a process for the preparation of the immunosuppressive compound tacrolimus. It also is directed to genetically modified strains of the microorganism Streptomyces tsukubaensis (S. tsukubaensis) and to an improved fermentation process for the preparation of tacrolimus (FK-506) or salts or derivatives thereof by cultivating these genetically modified strains and then isolating the immunosuppressive compound.

Furthermore, the invention relates to new genes encoding enzymes for the allylmalonyl-CoA biosynthetic pathway in particular in S. tsukubaensis and located on the tacrolimus biosynthesis gene cluster and to genetically modified strains of S. tsukubaensis, wherein these genes are overexpressed and/or inactivated. WO 2010/004304, Moss et al. describes strains producing FK-506 or FK-520.

Tacrolimus, which is also referred to as FK-506 (Fermentek catalogue number 506), is a 23-membered macrolide lactone and belongs to the group of polyketides. Tacrolimus was first isolated in the 1980's from the fermentation broth of the soil bacteria Streptomyces tsukubaensis. The antibiotic macrolide compound tacrolimus was e.g. reported in 1984 by Kino et al. (J. Antibiotics 40, 1249-1255, 1984). Later on tacrolimus was prepared as a microbial natural product by using different microorganisms, i.e. soil bacteria such as Streptomyces sp. MA6858 (U.S. Pat. No. 5,116,756) ATCC 55098, Streptomyces tsukubaensis NRRL 18488 (EP-B 0 356 399 and U.S. Pat. No. 5,200,411), Streptomyces clavuligerus CKD 1119 (KR-B 100485877) or Streptomyces glaucescens MTCC 5115 (US 2007191415).

The product tacrolimus exhibits immunosuppressive activities which are due to its effect to reduce the activity of the enzyme peptidyl-propyl isomerase and to the binding to the protein immunophilin FKBP12 (FK506 binding protein). Tacrolimus and the structurally similar polyketides ascomycin and rapamycin require initial binding to the highly conserved protein cyclophilin FKBP12 in order to be physiologically active. The rapamycin/FKBP12 complex binds to mTOR (mammalian target of rapamycin), a serine-threonine kinase that appears to act as a central controller for sensing the cellular environment and regulating translation initiation (see e.g. Easton J. B. and Houghton P. J., 2004, Expert Opin Ther Targets; 8(6):551-64). However, the tacrolimus/FKBP12 complex was found to bind to a different cellular target and inhibits the phosphatase activity of calcineurin, in analogy to cyclosporine (see Allison A. C., 2000, Immunopharmacology; 47(2-3):63-83).

Tacrolimus is often used for immunosuppression following e.g. organ transplantation. Furthermore, tacrolimus and its derivatives have been shown to be effective in treating a number of diseases such as asthma, inflammatory diseases and hyperproliferative skin disease. Tacrolimus and other immunosuppressant such as rapamycin, cyclosporine, or a combination thereof are also useful in the treatment of various auto-immmune diseases. For many years calcineurin inhibitors (e.g. cyclosporine and tacrolimus) have been the mainstay of immunosuppressive therapy. These two compounds are potent suppressors of cellular immune response and have significantly improved the outcome of organ transplants during the past two decades (see Allison A. C., 2000, Immunopharmacology; 47(2-3):63-83).

Gene clusters encoding the biosynthetic pathways of a great number of medically important drugs of microbial origin have already been cloned and sequenced, including the gene cluster of macrolides rapamycin, ascomycin and tacrolimus. With respect to cloning of the tacrolimus gene cluster, a partial sequence, mostly encompassing genes encoding polyketide synthase (PKS), was reported in the literature (see Motamedi H. and Shafiee A. 1998, Eur J Biochem; 256(3):528-34). On the other hand, scientists reported cloning of the ascomycin gene cluster in 2000 (see Wu K et al. 2000, Gene; 251(1):81-90, U.S. Pat. No. 6,503,737). Tacrolimus structurally and by the biosynthetic origin resembles ascomycin (FK520) and rapamycin (see Reynolds et al.; Drugs and the Pharmaceutical Sciences, 1997, 82, 497-520. They all can be synthesised by combined polyketide (PKS) and non-ribosomal peptide biosynthetic pathways (NRPS) (see McDaniel R et al. 2005, Chem Rev; 105(2):543-58).

Tacrolimus and ascomycin are structurally similar. As only structural difference, the allyl side chain at carbon 21 of tacrolimus is replaced by an ethyl side chain in ascomycin. The structures of tacrolimus (FK506) and ascomycin (FK520) compounds are shown as formulae (Ia) and (Ib).

The structures of ascomycin and tacrolimus already suggest complex biosynthetic pathways which can be divided into four steps considering the biosynthetic mechanism:

    • 1. chain initiation using the unusual shikimate derived starter,
    • 2. chain elongation common to most PKS derived compounds,
    • 3. chain termination and cyclization by incorporation of L-pipecolic acid and
    • 4. post-PKS processing.

During the tacrolimus fermentation process, undesired ascomycin (FK520) product is also produced as an impurity, thus lowering the final yield of tacrolimus and causing significant additional costs to the downstream isolation processes of tacrolimus.


FK506, R═—CH2—CH═CH2  (Ia)
FK520, R═CH2—CH3  (Ib)

In particular, the present invention relates to the use of a compound of formula (Ia) or of formula (Ib) as defined above or an optical isomer, pharmaceutically acceptable salt, hydrate, solvate or polymorph thereof for the preparation of a medicament and for the treatment of a mammal, including humans. The invention relates to the use of a compound for the preparation of a medicament for the prevention and/or treatment of a condition or disease in an animal, including a human.

Ethylmalonyl-CoA is a known important building unit for ascomycin (FK-520) biosynthesis. The following genes which are located at the biosynthesis ascomycin cluster found in S. hygroscopius and involved in ascomycin biosynthesis are reported in the state of the art (see Liu et al., Journal of Bacteriology, 1999, 181, 6806-6813; Liu et al., Metabolic Engineering, 2001, 3, 40-48) and seem to be relevant:

    • a) gene encoding crotonyl-CoA reductase (ccr gene),
    • b) gene encoding B12 dependent isobutyryl-CoA mutase (icm gene),
    • c) gene encoding ethylmalonyl-CoA mutase (ecm gene).

The biosynthetic pathways providing the ethylmalonyl-CoA extender unit in specific stages of polyketide chain assembly of several polyketide-derived compounds are described in the state of the art (see Wu et al., loc. cit.; Reynolds et al., loc. cit.). It seems that the ethylmalonyl-CoA extender unit is derived by the reaction of carboxylation of butyryl-CoA. At least two pathways leading to butyryl-CoA have been identified in Streptomycetes. One pathway involves a condensation of two acetate units, thus forming acetoacetate-CoA activated product, which is further processed to crotonyl-CoA and through a key step of reduction of crotonyl-CoA to butyryl-CoA, catalyzed by a crotonyl-CoA reductase (ccr) (see Wallace K. K. et al. 1995, Eur J Biochem; 233:954-962). This gene was first identified in S. collinus where it was found to be located within a set of primary metabolic genes. Later on, its homologues were identified within biosynthetic clusters encoding several compounds that require ethylmalonyl-CoA as a precursor (see Cropp et al., 2001, J Ind Microbiol Biotechnol; 27:368-377).

Recently, a ccr homologue in Rhodobacter sphaeroides was shown to encode an enzyme with crotonyl-CoA carboxylase/reductase activity, catalyzing reductive carboxylation of crotonyl-CoA to ethylmalonyl-CoA (see Erb T. J. et al. 2007, Proc Natl Acad Sci USA; 25: 10631-10636). Moreover, this enzyme was shown to be a part of a newly discovered acetate assimilation pathway termed “ethylmalonyl-CoA pathway” which enables growth of microorganisms lacking isocitrate lyase gene on acetate as the only carbon source. This pathway is predicted to involve several steps. It is initiated, similarly to previous predictions, by condensation of two acetyl-CoA units and subsequent processing to crotonyl-CoA. Crotonyl-CoA is then converted by Ccr directly to (2S)-ethylmalonyl-CoA which is first epimerized to (2R)-ethylmalonyl-CoA and later converted to methylsuccinyl-CoA by a vitamin B12-dependent ethylmalonyl-CoA mutase (ecm) (see Erb T. J. et al. 2008, J Biol Chem; 283: 32283-32293). Subsequently, methylsuccinyl-CoA is converted to mesaconyl-CoA by methylsuccinyl-CoA dehydrogenase and in the next step mesaconyl-CoA is converted to β-methylmalyl-CoA by mesaconyl-CoA dehydratase. Finally, β-methylmalyl-CoA is cleaved to glyoxylate and propionyl-CoA which then enter previously known metabolic pathways. Glyoxylate can be condensed with acetyl-CoA to yield malate and propionyl-CoA can be carboxylated to methylmalonyl-CoA and then succinyl-CoA. Interestingly, several Streptomyces species encode some of the genes involved in the ecm pathway as a cluster suggesting that this pathway is active in Streptomyces while growing on acetate butyrate or fatty acids as a single carbon source (see Akopiants K. et al. J Ind Microbiol Biotechnol; 33: 141-150).

A second pathway is proposed which proceeds through an isomerization step of a valine metabolite, isobutyryl-CoA, to form butyryl-CoA and is catalyzed by the coenzyme B12-dependent isobutyryl-CoA mutase (icm) (see Reynolds K. et al. 1988, J Chem Soc Perkin Trans 1; 3195-3207; and Zerbe-Burkhardt K. et al. 1998, J Biol Chem; 273:6508-6517).

The metabolic origin of allylmalonyl-CoA precursor and genes involved in its biosynthesis for tacrolimus (FK506) producing organisms have not been identified in the prior art.

The invention provides a new biosynthetic pathway for the provision of allylmalonyl-CoA. Surprisingly, a group of genes was found responsible for allylmalonyl-CoA biosynthesis, which is positioned in the left arm of the FK506 polyketide synthase (PKS) cluster. The newly obtained sequence of the extreme left side of the FK506-biosynthesis gene cluster was found to encode genes involved in allylmalonyl-CoA biosynthesis and is referred to as “Allyl(AII) cluster” or “Allyl(AII) subcluster” of the tacrolimus gene cluster (see Table 1).

The present invention relates to this novel nucleotide sequences containing genes, involved in the biosynthesis of allylmalonyl-CoA precursor (building block), which are located at the left side of the FK506 polyketide synthase (PKS) gene cluster.

The various uses of these sequences for the improvement of FK506 producing strains, in particular in terms of yields and purity, are also included in the present invention. The invention also provides a genetically modified strain having heterogeneously expressed “Allyl subcluster” that allows selective production of tacrolimus, ascomycin or related compounds.

It is one object of the present invention to provide an improved process for production of tacrolimus by reducing or abolishing the formation of by-products such as ascomycin and/or by increasing the yield of production of tacrolimus.

It was found that the availability of the extender unit allylmalonyl-CoA versus ethylmalonyl-CoA plays an important role in the final ratio of the wanted product tacrolimus (FK506) or respectively ascomycin (FK520) as by-product at the end of the fermentative process. The invention therefore provides several possibilities how to control the ratio of said extender units resulting in significantly improved ratios of the wanted product and by-products.

In this aspect, the present invention describes an improved fermentative preparation of tacrolimus carried out by genetically modified strain preferably by Streptomyces tsukubaensis (NRRL 18488) in which the biosynthesis of the product ascomycin (FK520) may be significantly reduced or abolished. Preferably, the yield of tacrolimus remains either constant or is increased. Thus, the process significantly reduces the disadvantages of known processes of fermentative production by employing means to reduce (or abolish) ethylmalonyl-CoA supply and/or by increasing the allylmalonyl-CoA biosynthesis. The process can reduce (or abolish) ascomycin production, and maintain or increase the production yield of tacrolimus.

The final ratios of tacrolimus on the one hand and of ascomycin on the other hand at the end of the process can be regulated by inactivating and/or over expressing these genes involved in the metabolism of ethylmalonyl-CoA and/or allylmalonyl-CoA.

Furthermore, the present application is directed to genetically modified strain of a microorganism, wherein the genetic material of the microorganism comprises at least one inactivated and/or over expressed gene involved in the metabolism and/or the biosynthesis of ethylmalonyl-CoA and/or allylmalonyl-CoA.

DETAILED DESCRIPTION OF INVENTION

The present invention is directed to a process for the preparation of tacrolimus, wherein the process comprises the step of cultivation of a genetically modified strain of a microorganism, preferably belonging to the genus Streptomyces, more preferably a genetically modified strain of Streptomyces tsukubaensis, wherein the genetic material of the microorganism comprises at least one inactivated and/or over expressed gene involved in the metabolism and/or the biosynthesis of ethylmalonyl-CoA and/or allylmalonyl-CoA.

The present invention also describes a genetically modified strain of a microorganism belonging to the genus Streptomyces, wherein the genetic material of the microorganism comprises at least one inactivated and/or over expressed gene involved in the metabolism and/or the biosynthesis of ethylmalonyl-CoA and/or allyl malonyl-CoA.

In particular the process for the preparation of tacrolimus according to the present application comprises at least one of the following steps:

    • a) Generation of genetically modified strain of a microorganism;
    • b) Preparation of seed medium comprising addition of genetically modified strain of a microorganism into a nutrient medium and cultivating said strain of a microorganism;
    • c) Main fermentation comprising addition of seed medium of genetically modified strain of a microorganism into a nutrient medium in a bioreactor, cultivating said strain of a microorganism and production of tacrolimus;
    • d) Separation and purification of product from the fermentation broth (harvest).

In particular the process for the preparation of tacrolimus according to the present invention comprises the generation of genetically modified strain of a microorganism, which is described in the present application, preparation of seed medium and main fermentation comprising cultivating said genetically modified strain of a microorganism. Preferably the process for the preparation of tacrolimus according to the present application comprises the steps a) to d) as mentioned above. The process steps a) to d) are described in more detail below.

In a preferred embodiment the invention deals with a process for the preparation of tacrolimus as mentioned above, wherein the process comprises the step of cultivation of a genetically modified strain of a microorganism wherein the microorganism is a bacterium preferably selected from genus Streptomyces. In particular the said microorganism may be selected from order Actinomycetales. Preferred is a microorganism belonging to order Actinomycetales having PKS activity or having heterologously expressed PKS or part thereof. More particularly the microorganism may be selected from the genus Streptomyces. Particularly Streptomyces tsukubaensis, Streptomyces sp. ATCC 55098 or Streptomyces hygroscopicus var. ascomyceticus ATCC 14891 may be used.

In particular the microorganism is selected from a genetically modified strain of Streptomyces tsukubaensis, preferably Streptomyces tsukubaensis (NRRL 18488). Further, the microorganism may be selected from a genetically modified strain of Streptomyces hygroscopius.

Moreover, it is also contemplated to use the following microorganisms for carrying out the process of the present invention: Streptomyces tsukubaensis No. 9993 (Ferm BP-927), Streptomyces hygroscopicus subsp. hygroscopicus (DSM 40822), Streptomyces sp. AA6554, Streptomyces hygroscopicus var. ascomyceticus MA 6475 ATCC 14891, Streptomyces hygroscopicus var. ascomyceticus MA 6678 ATCC 55087, Streptomyces hygroscopicus var. ascomyceticus MA 6674, Streptomyces hygroscopicus var. ascomyceticus ATCC 55276, Streptomyces hygroscopicus subsp. ascomyceticus ATCC 14891, Streptomyces kanamyceticus KCC S-0433, Streptomyces clavuligerus CKD1119, Streptomyces hygroscopicus subsp. yakushimaensis, Streptomyces sp. DSM 7348, Micromonospora n.sp. A92-306401 DSM 8429, Streptomyces sp. MA 6548 and Streptomyces sp. MA 6858 ATCC 55098.

In another aspect the invention relates to a process for the preparation of tacrolimus as described in the present application, wherein the process comprises the step of cultivation of a genetically modified strain of a microorganism preferably belonging to the genus Streptomyces, wherein the process is carried out under the external addition of allylmalonyl-CoA and/or at least one precursor of allylmalonyl-CoA. In particular allylmalonyl-CoA and/or at least one precursor of allylmalonyl-CoA are added to the fermentation medium in the main fermentation process (step c) as described above.

Furthermore, the fermentative process described in the present application may comprise cultivating a genetically modified strain of a microorganism preferably belonging to the genus Streptomyces, more preferably a genetically modified strain of Streptomyces tsukubaensis, as provided by this invention, and adding in a controlled manner allylmalonyl-, ethylmalonyl-, and/or propylmalonyl-CoA and/or precursors of allylmalonyl-, ethylmalonyl-, and/or propylmalonyl-CoA to the fermentation medium. Substantially pure tacrolimus, ascomycin or related compounds respectively, can be thus obtained. In this sense a genetically modified strain of a microorganism preferably belonging to the genus Streptomyces, more preferably a genetically modified strain of Streptomyces tsukubaensis, having inactivated at least AIIR gene according to SEQ.ID.#4, has to be used.

In another embodiment the process for the preparation of tacrolimus as described in the present application comprises the step of cultivation of a genetically modified strain of a microorganism, preferably belonging to the genus Streptomyces, more preferably a genetically modified strain of Streptomyces tsukubaensis, wherein the genetic material of the microorganism comprises at least one inactivated and/or over expressed gene selected from gene sequence of Allyl-subcluster according to SEQ.ID.#1, which is composed of the following genes AIIA gene according to SEQ.ID.#2, AIIK gene according to SEQ.ID.#3, AIIR gene according to SEQ.ID.#4, AIID gene according to SEQ.ID.#5, AIIM gene according to SEQ.ID.#6, AIIN gene according to SEQ.ID.#7, AIIP gene according to SEQ.ID.#8, AIIO gene according to SEQ.ID.#9, and AIIS gene according to SEQ.ID.#10. The nucleotide sequences mentioned above are described in table 1 and listed in the appendix.

The entire gene cluster encoding ORFs (open reading frame) required for the biosynthesis of FK506 was sequenced. In addition to the published sequence of the central part of the cluster which contains the PKS (polyketide synthase) genes (see Motamedi H. and Shafiee A. 1998, Eur J Biochem; 256(3):528-34), the sequences of the genes present to the left and right fringe of the polyketide synthase cluster were obtained and annotated. On the left side of the gene cluster, a number of ORFs were identified, the majority of which did not show any homology to the genes present in the ascomycin (FK520) biosynthesis cluster (see Wu K et al. 2000, Gene; 251(1):81-90, U.S. Pat. No. 6,503,737). BLAST search using these ORFs as a query revealed the putative functions of the identified genes as presented in the Table 1.

This Allyl-cluster (or Allyl-subcluster) encoding genes are involved in the biosynthesis of allylmalonyl-CoA precursor specifically required for the biosynthesis of tacrolimus. Further, it was found that the Allyl-subcluster encoding genes are involved in the biosynthesis of ethylmalonyl-CoA.

In a further aspect, the invention deals with nucleotide sequences of Allyl-subcluster involved in ethylmalonyl-CoA or allylmalonyl-CoA biosynthesis of an microorganismen belonging to the genus Streptomyces comprising the sequence according to SEQ.ID #1, which is composed of several genes according to SEQ.ID #2 to SEQ.ID #10, and variants thereof comprising one or more nucleotide additions, deletions, substitutions or inversions. The nucleotide sequences of Allyl-subcluster are shown in table 1 and listed in appendices (SEQ.ID #1 to SEQ.ID #10).

TABLE 1 Organization of the Allylmalonyl-CoA Biosynthesis Part (Allyl cluster or All-cluster) of the Tacrolimus Gene Cluster Gene Length Length Start Stop SEQ. ID. # Name Gene Function Start Stop (bp) (AA) Codon Codon 2 AllA Acyltransferase and 2775 4067 1551 517 ATG TGA acyl-Carrier Protein 3 AllK Ketoacyl synthase 4078 6465 2428 776 ATG TGA 4 AllR Acyl CoA reductase 6465 7799 1335 445 ATG TGA 5 AllD Acyl-CoA 7799 8956 1158 386 GTG TAG dehydrogenase 6 AllM Methionine gamma 10126 8975 1152 384 ATG TGA lyase 7 AllN Transcriptional 10186 10650 465 155 ATG TAG regulator 8 AllP P450 10757 11983 1326 442 CTG TAG monooxygenase 9 AllO Acyl-CoA 12171 13358 1185 395 GTG TGA oxidoreductase 10 AllS Acetoacetyl-CoA 13467 14120 654 218 GTG TGA reductase

It was found that by blocking synthesis of ethylmalonyl-CoA and allylmalonyl-CoA in a mutant strain, a new process is possible in which by feeding these building blocks one can control which polyketide is produced. It was found that inactivation of AIIR gene encoding oxidoreductases (similar to crotonyl-CoA reductase) entirely abolished the production of tacrolimus. However external feeding with allylmalonyl-CoA precursors enables exclusive production of tacrolimus, with abolished production of ascomycin in the fermentation broth. It was also found that inactivation of AIIR gene entirely abolished the production of ascomycin (FK-520). However with external feeding of ethylmalonyl-CoA precursors enables exclusive production of ascomycin (FK-520), with abolished production of tacrolimus in the fermentation broth.

This process is possible in any ascomycin or tacrolimus producing organism. Method for blocking synthesis of ethylmalonyl-CoA in an ascomycin producing organism is well known to a person skilled in art, as genes responsible for ethylmalonyl-CoA biosynthesis have been elucidated in ascomycin producing organisms (Wu et al. 2000, Gene 251, 81-90). Inactivation of ccr homologues would be the first step in preparation of such organism. Since PKS for synthesis for ascomycin and tacrolimus are highly homologous, the promiscuity of module 7, incorporating allylmalonyl-CoA or ethylmalonyl-CoA can be expected for PKS of all ascomycin/tacrolimus producing organisms.

In one embodiment of the invention the process for the preparation of tacrolimus as described in the present application comprises the step of cultivation of a genetically modified strain of a microorganism belonging to the genus Streptomyces, preferably a genetically modified strain of Streptomyces tsukubaensis, wherein the process is carried out under the external addition of allylmalonyl-CoA and/or at least one precursor of allylmalonyl-CoA.

Different allylmalonyl-CoA precursors can be used. More particularly the addition of allylmalonyl-SNAC (allylmalonyl-(N-acetyl-cysteamine)thioester) is preferred. In terms of the present invention allylmalonyl-CoA precursors also includes analogues of allylmalonyl-CoA.

Alternatively, allylmalonic acid or analogue thereof can be directly used in said process given additional genetic modification of the strain used for the process. In this case malonyl-CoA synthetase and dixarboxylate carrier protein have to be expressed in the used microorganism. An example of genetically modified microorganism capable of incorporation of dicarboxylate compounds provided in the growth medium is described by Lombo et al. Biotechnol. Prog. 2001, 17, 612-617. Sufficient activity of malonyl-CoA synthetase for allylmalonic acid as a substrate is described by Pohl et al. J. Am. Chem. Soc. 2001, 123, 5822-5823.

In particular the process as described above comprises the step of cultivation of a genetically modified strain of a microorganism belonging to the genus Streptomyces, wherein the genetic material of the microorganism comprises at least one inactivated and/or over expressed gene selected from the group of

    • AIIK gene according to SEQ.ID.#3 and
    • AIIR gene according to SEQ.ID.#4.

In further embodiment of the invention the process as described above comprises the step of cultivation of a genetically modified strain of a microorganism belonging to the genus Streptomyces, preferably to a genetically modified strain of Streptomyces tsukubaensis, wherein the genetic material of the microorganism comprises additionally inactivated gene ccr gene according to SEQ.ID.#11.

In this particular aspect the invention relates to the following strains of Streptomyces tsukubaensis:

    • a) Streptomyces tsukubaensis F499
      • deposited with the deposition number DSM 22507 on 23 Apr. 2009, at the DSMZ—Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganism and Cell Cultures) in Braunschweig/Germany. This strain is described as NRRL 18488 ΔaIIR.
    • b) Streptomyces tsukubaensis F872
      • deposited with the deposition number DSM 22509 on 23 Apr. 2009, at the DSMZ—Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganism and Cell Cultures) in Braunschweig/Germany. This strain is described as NRRL 18488 ΔaIIK.

In a further embodiment of the invention the process as described above comprises the step of cultivation of a genetically modified strain of a microorganism belonging to the genus Streptomyces, preferably to a strain of Streptomyces tsukubaensis, wherein the genetic material of the microorganism comprises at least one inactivated gene selected from Allyl-subcluster according to SEQ.ID.#1, which is composed of the following genes AIIA gene according to SEQ.ID.#2, AIIK gene according to SEQ.ID.#3, AIIR gene according to SEQ.ID.#4, AIID gene according to SEQ.ID.#5, AIIM gene according to SEQ.ID.#6, AIIN gene according to SEQ.ID.#7, AIIP gene according to SEQ.ID.#8, AIIO gene according to SEQ.ID.#9, and AIIS gene according to SEQ.ID.#10, and wherein the process is carried out under the external addition of allylmalonyl-CoA and/or at least one precursor of allylmalonyl-CoA.

In a preferred embodiment the process as described above comprises the step of cultivation of a genetically modified strain of a microorganism belonging to the genus Streptomyces, wherein the genetic material of the microorganism comprises at least one inactivated gene selected from the group of AIIK gene according to SEQ.ID.#3 and AIIR gene according to SEQ.ID.#4, and wherein the process is carried out under the external addition of allylmalonyl-CoA and/or at least one precursor of allylmalonyl-CoA.

In a preferred embodiment the process as described above comprises the step of cultivation of a genetically modified strain of a microorganism belonging to the genus Streptomyces, preferably to a genetically modified strain of Streptomyces tsukubaensis, wherein the genetic material of the microorganism comprises inactivated AIIR gene according to SEQ.ID.#4 and inactivated ccr gene according to SEQ.ID.#11, and wherein the process is carried out under external addition of allylmalonyl-CoA and/or at least one precursor of allylmalonyl-CoA.

Further the present invention relates to a nucleotide sequence encoding one or several gene(s) involved in the metabolism and/or the biosynthesis of ethylmalonyl-CoA and/or allylmalonyl-CoA of an microorganism belonging to the genus Streptomyces, comprising the sequence according to SEQ ID #1, which is composed of the following genes AIIA gene according to SEQ.ID.#2, AIIK gene according to SEQ.ID.#3, AIIR gene according to SEQ.ID.#4, AIID gene according to SEQ.ID.#5, AIIM gene according to SEQ.ID.#6, AIIN gene according to SEQ.ID.#7, AIIP gene according to SEQ.ID.#8, AIIO gene according to SEQ.ID.#9, and AIIS gene according to SEQ.ID.#10, and variants thereof comprising one or more nucleotide addition(s), deletion(s), substitution(s) and/or inversion(s).

In particular the nucleotide sequence as described above has at least 50% nucleotide identity with SEQ. ID.#1.

Also provided by the invention is a nucleotide sequence as described above wherein the nucleotide sequence has at least 60% nucleotide identity, preferably at least 70%, preferably at least 80%, preferably at least 90% with sequence according to SEQ.ID #1, which is composed of several genes according to SEQ.ID #2 to SEQ.ID10#. The above described variants of the nucleotide sequences should retain the capacity to encode the enzymes involved in the ethylmalonyl- or allylmalonyl-CoA biosynthesis of an organism belonging to the genus Streptomyces.

In this sense the invention provides nucleotide sequence of every individual gene as listed in Table 1 and described in SEQ.ID #2 to SEQ.ID #10 and their amino acid products described in SEQ.ID #13 to SEQ.ID #21 and variants thereof comprising one or more nucleotide addition(s), deletion(s), substitution(s) and/or inversion(s), wherein the nucleotide sequence has at least 50% nucleotide identity, preferably at least 60%, preferably at least 70%, preferably at least 80%, preferably at least 90% with sequence according to sequence which is composed of several genes according to SE D #2 to SEQ.ID10#.

The proposed biosynthetic pathway can be described as follows. In order to obtain allylmalonyl-CoA, a C5 precursor, valeryl-CoA or 4-pentenoyl-CoA should first be formed. Analogously to ethylmalonyl-CoA, originating from two acetate units through acetoacetate and crotonyl-CoA, propylmalonyl-CoA or allylmalonyl-CoA can emerge from one 3-carbon and one 2-carbon unit. The genes AIIA (acyltransferase) and AIIK (ketosynthase) have been identified, which carry out condensation reaction as single-step by a rather short polyketide synthase (PKS)-like enzyme complex. It is not clear, how 5-carbon intermediate (3-oxopentanoic acid or its reduced intermediate) is activated by the addition of CoA or is transferred directly to the FK506 PKS complex, before it is further processed to the final allylmalonyl-CoA, a C5-precursor. Feeding experiments with final synthetic allyl precursor however indicate ability of FK506 PKS to incorporate the extender in the final allylmalonyl-CoA form. The putative AIIS gene, homologous to acetoacetyl-CoA reductase, carries out the first reduction step yielding 3-hydroxypentanoyl-CoA. Additional oxidoreductases (AIIR—similar to crotonyl-CoA carboxylase/reductase, AIID and AIIO) can then further reduce this compound to propylmalonyl-CoA and in concert with the AIIP, P450 monooxygenase, also introduce an —OH group and subsequently a double bond in the position 4, yielding allylmalonyl-CoA. This is then introduced to the nascent polyketide chain by the corresponding acyltransferase (AT4) gene on the PKS module 4. As a part of the Allyl cluster, ORF designated as AIIM were identified. This gene product shows homology to the methionine gamma lyase and likely converts methionine to 2-oxobutyrate that readily metabolizes to propionyl-CoA, a starter unit required for biosynthesis of the first 5-carbon intermediate by the AIIA. Propionyl-CoA precursor can be limiting during secondary metabolism.

Therefore, the presence of the AIIM gene product is likely needed for sufficient provision of propionyl-CoA in order to increase the yield of the final product FK-506.

The proposed pathway also explains the origin of the ethylmalonyl-CoA and thereby also the origin of FK-520 in fermentation broths of FK-506-producing microorganisms. Genes, present in the >>Allyl subcluster<< of the FK-506 biosynthetic cluster of S. tsukubaensis, involved in biosynthesis of allylmalonyl-CoA, can also produce ethylmalonyl-CoA. Namely the enoyl CoA reductase (gene AIIR) most probably shows limited promiscuity to acetoacetate (C4) unit instead of the C5 unit (3-oxopentanoic acid or its reduced intermediate), which is then processed in a similar manner as in the pathway, described above. The subsequent steps proceed in a similar manner for both precursors; however, the C4 unit seems not to be a substrate for P450 mediated hydroxylation and formation of the double bond. Deletion of enoyl-CoA reductase/carboxylase (AIIR) gene was found to completely abolish this biosynthetic pathway and production of FK-506 and FK-520. Deletion of ketoacyl synthase (AIIK) gene was found to completely abolish only production of FK-506, production of FK-520 remain on the level of wild type S. tsukubaensis strain.

Interestingly, the reaction steps described above leading to ethylmalonyl-CoA and allylmalonyl-CoA (or propylmalonyl-CoA) extender units for FK-520/FK-506 biosynthesis, mechanistically closely resemble the initial reactions of the “ethylmalonyl-CoA pathway” up to the point where ethymalonyl-CoA intermediate is formed. This primary metabolic pathway is most probably involved in the growth of most Streptomyces species on acetate as the sole carbon source and involves ethylmalonyl-CoA as an intermediate compound, produced by crotonyl-CoA carboxylase/reductase (ccr), which is further converted to methylsuccinyl-CoA by ethylmalonyl-CoA mutase (ecm). Clearly, one would expect that this pathway, if active under the given growth conditions, can also represent an important source of ethylmalonyl-CoA in S. tsukubaensis. However, many genes encoding “ethylmalonyl-CoA pathway”, including ccr—which produces ethylmalonyl-CoA- and ecm—which processes it further—are located in the same operon in Streptomyces and are most likely co-transcribed. Such gene architecture is ideal when both genes must act in concert and substrates must be rapidly passed through the metabolic pathway to end-products, but may come short of providing sufficient amounts of a single intermediate, namely ethylmalonyl-CoA, as a building block for secondary metabolism. This may provide an explanation why many gene clusters for polyketide biosynthesis, which require ethylmalonyl-CoA as an extender unit, also contain an additional copy of a ccr gene homologue, in this context without the ecm gene that would immediately consume ethylmalonyl-CoA produced.

Although the reactions involved are mechanistically similar, the enzymes providing allylmalonyl-CoA (propylmalonyl-CoA) and ethylmalonyl-CoA as building blocks for FK-506 and FK-520 biosynthesis in S. tsukubaensis and the enzymes of the “ethylmalonyl-CoA pathway” of this organism differ in one important aspect. While “ethylmalonyl-CoA pathway” specifically involves ethylmalonyl-CoA intermediate and only small amounts of propylmalonyl-CoA might eventually be formed, the enzymes encoded by the all subcluster show a different specificity. They predominantly produce allylmalonyl-CoA (propylmalonyl-CoA) while ethylmalonyl-CoA is produced in small amount. The amounts are probably relatively small because some enzymes of the pathway (namely AIIR) can accept 4-carbon and 5-carbon intermediates with similar efficiency while others might be very specific for substrates leading exclusively to allylmalonyl-CoA (propylmalonyl-CoA). In the context of a fermentative process for production of FK-506 by Streptomyces enzymes both metabolic systems may be expressed although their expression is most probably induced by completely different factors. While genes of the all subcluster are probably transcribed together with other genes of the FK-506 biosynthetic cluster once secondary metabolism is induced, the expression and activity of “ethylmalonyl-CoA pathway” enzymes is most likely dependent on growth conditions, most importantly on the composition of the growth medium.

Clearly, in order for concentration of ethylmalonyl-CoA and thereby yield of FK-520 to be kept as low as possible, the composition of growth medium should be adapted so that the genes of the “ethylmalonyl-CoA pathway” are not transcribed or are transcribed at minimum level. Alternatively, the expression of enzymes which take part in the ecm pathway and which are usually encoded on the same operon in Streptomyces, has to be engineered in order to keep ethylmalonyl-CoA concentrations low. The ccr gene encoding crotonyl-CoA carboxylase/reductase should be inactivated while the other four genes encoding ethylmalonyl-CoA mutase (ecm), methylsuccinyl-CoA dehydrogenase, mesaconyl-CoA dehydratase and β-methylmalyl-CoA lyase should be overexpressed using a strong consitutive promoter. However, if complete abolishment of ethylmalonyl-CoA in the cells is desired independently of growth conditions and medium, it may be necessary to introduce target mutations which interrupt both pathways at the same mechanistic step. As described in this invention, this step may be the inactivation of both ccr homologues, the ccr gene of the “ethylmalonyl-CoA pathway” as well as the aIIR gene of the all subcluster involved predominantly in the provision of allylmalonyl-CoA (propylmalonyl-CoA).

One object of invention is to provide a process for the preparation of tacrolimus, wherein the process comprises the step of cultivation of a genetically modified strain of a microorganism, preferably belonging to the genus Streptomyces, more preferably a genetically modified strain of Streptomyces tsukubaensis, wherein the genetic material of the microorganism is modified so that it improves ratio of intracellular pool of allylmalonyl-CoA versus ethylmalonyl-CoA.

In this embodiment the process for the preparation of tacrolimus as described in the present invention comprises the step of cultivation of a genetically modified strain of a microorganism, preferably belonging to the genus Streptomyces, more preferably a genetically modified strain of Streptomyces tsukubaensis, wherein the genetic material of the microorganism comprises at least one over expressed gene selected from gene sequence of Allyl-subcluster according to SEQ.ID.#1, which is composed of the following genes AIIA gene according to SEQ.ID.#2, AIIK gene according to SEQ.ID.#3, AIIR gene according to SEQ.ID.#4, AIID gene according to SEQ.ID.#5, AIIM gene according to SEQ.ID.#6, AIIN gene according to SEQ.ID.#7, AIIP gene according to SEQ.ID.#8, AIIO gene according to SEQ.ID.#9, and AIIS gene according to SEQ.ID.#10. The nucleotide sequences mentioned above are described in table 1 and listed in the appendix.

The present application involves the generation of the S. tsukubaensis strain(s) with inactivated and/or over expressed one or several of the genes listed in Table 1, encoding proteins necessary for allylmalonyl-CoA and/or ethylmalonyl-CoA precursor synthesis.

More particularly in this aspect the present invention is directed to the generation of genetically modified strain of Streptomyces tsukubaensis wherein the strain comprises at least one inactivated gene involved in the provision of key building units for tacrolimus (FK-506) and/or ascomycin (FK-520) biosynthesis. These genetically modified strains have been found to be useful for the improved production of tacrolimus.

Methods for genetically modification of a microorganism are known in the art, e.g. amplification of gene copy number. Another example is insertion of additional copies of said genes under control of a strong promoter. Yet another example in this sense is modification of activity of transcriptional regulator found in the “AII” subcluster.

In this sense the invention provides an improved strain of Streptomyces tsukubaensis for fermentative production of tacrolimus by improving intracellular pool of allylmalonyl-CoA precursor and or reducing intracellular pool of ethylmalonyl-CoA. The novel nucleotide sequences according to table 1 and SEQ. ID #1, can be used to regulate the expression of said genes involved in biosynthesis of allylmalonyl-CoA.

In one embodiment of the invention the process for the preparation of tacrolimus as described in the present application comprises the step of cultivation of a genetically modified strain of a microorganism, wherein the genetic material of the microorganism comprises at least one inactivated and/or over expressed gene selected from crotonyl-CoA reductase (ccr) gene according to SEQ.ID.#11, and ethylmalonyl-CoA mutase (ecm) according to SEQ.ID.#12. Nucleotide sequences are listed in the appendix.

The present application is directed to a genetically modified strain of a microorganism belonging to the genus Streptomyces, preferably a genetically modified strain of Streptomyces tsukubaensis, wherein the genetic material of the microorganism comprises at least one inactivated and/or over expressed gene involved in the metabolism and/or the biosynthesis of ethylmalonyl-CoA and/or allylmalonyl-CoA.

In particular the present application is directed to a genetically modified strain of a microorganism belonging to the genus Streptomyces as described above, wherein the genetic material of the microorganism comprises at least one inactivated and/or over expressed gene selected from gene sequence of Allyl-subcluster according to SEQ.ID.#1, which is composed of the following genes AIIA gene according to SEQ.ID.#2, AIIK gene according to SEQ.ID.#3, AIIR gene according to SEQ.ID.#4, AIID gene according to SEQ.ID.#5, AIIM gene according to SEQ.ID.#6, AIIN gene according to SEQ.ID.#7, AIIP gene according to SEQ.ID.#8, AIIO gene according to SEQ.ID.#9, and AIIS gene according to SEQ.ID.#10.

In particular the present invention is directed to a genetically modified strain of a microorganism belonging to the genus Streptomyces as described above, preferably a genetically modified strain of Streptomyces tsukubaensis, wherein the genetic material of the microorganism comprises at least one overexpressed gene selected from the group of AIIA gene according to SEQ.ID.#2, AIIK gene according to SEQ.ID.#3 and AIIR gene according to SEQ.ID.#4.

In particular the present application is directed to a genetically modified strain of a microorganism belonging to the genus Streptomyces as described above, preferably a genetically modified strain of Streptomyces tsukubaensis, wherein the genetic material of the microorganism comprises at least one overexpressed gene selected from the group of AIIA gene according to SEQ.ID.#2 and AIIK gene according to SEQ.ID.#3.

In another, yet similar embodiment, the novel nucleotide sequences containing genes, involved in the biosynthesis of allylmalonyl-CoA precursor allow a person skilled in the art the construction of recombinant strains for production of tacrolimus. In this sense any ascomycin producer microorganism can be engineered to produce tacrolimus. A suitable microorganism in this sense may be but is not limited to Streptomyces hygroscopicus. This can be achieved by transfer of said nucleotide sequences to said host strain by methods known in the art.

Further, present invention deals with a genetically modified strain of a microorganism, wherein said strain has a native or engineered polyketide synthase activity.

The present invention also relates to a genetically modified strain of Streptomyces tsukubaensis, wherein the genetic material of the microorganism comprises at least one inactivated and/or over expressed gene selected from the group of

    • AIIR gene according to SEQ.ID #4, encoding distant homologue of the crotonyl-CoA reductase,
    • AIIP gene according to SEQ.ID #8, encoding a cytochrome P450 enzyme,
    • AIIA gene according to SEQ. ID #2, encoding an acyltransferase enzyme and acyl carrier protein,
    • AIIK gene according to SEQ. ID #3, encoding a ketoacyl synthase enzyme,
    • AIID gene according to SEQ.ID.#5, encoding an acyl-CoA dehydrogenase enzyme,
    • AIIM gene according to SEQ. ID #6, encoding a Methionie gamma lyase enzyme and acyl carrier protein,
    • AIIN gene according to SEQ. ID. #7, encoding a transcriptional regulator,
    • AIIO gene according to SEQ. ID #9, encoding an Acyl-CoA oxidoreductase enzyme, and
    • AIIS gene according to SEQ.ID #10, encoding an acetoacetyl-CoA reductase enzyme.

The nucleotide sequences (DNA sequences) of the genes and the amino acid sequences of the gene products are shown in the appendix SEQ.ID #2 to SEQ.ID #10 and SEQ.ID #13 to SEQ. ID #21, respectively.

In this particular aspect the invention relates to the following strains of Streptomyces tsukubaensis:

    • a) Streptomyces tsukubaensis F499
      • deposited with the deposition number DSM 22507 on 23 Apr. 2009, at the DSMZ—Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganism and Cell Cultures) in Braunschweig/Germany. This strain is described as NRRL 18488 ΔaIIR
    • b) Streptomyces tsukubaensis F872
      • deposited with the deposition number DSM 22509 on 23 Apr. 2009, at the DSMZ—Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganism and Cell Cultures) in Braunschweig/Germany. This strain is described as NRRL 18488 ΔaIIK,
    • c) Streptomyces tsukubaensis F917
      • deposited with the deposition number DSM 22511 on 23 Apr. 2009, at the DSMZ—Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganism and Cell Cultures) in Braunschweig/Germany. This strain is described as NRRL 18488 AIIP+.

Furthermore, the nucleotide sequences containing genes involved in the biosynthesis of allylmalonyl-CoA precursor can be used to produce novel, hybrid polyketides. This can be achieved by transfer of said nucleotide sequences to any polyketide producing host strain microorganism by methods known in the art. Due to promiscuity of polyketide synthase (PKS) modules which is well known, one can expect at least traces of new hybrid polyketide compounds having allyl side chain in at least one carbon position.

The microorganism, which can be used for the genetic modification (over expression or inactivation of the said genes) may be selected from bacteria. More particularly the said microorganism is selected from order Actinomycetales. Preferred is a microorganism belonging to order Actinomycetales having PKS (polyketide synthase) activity. Alternatively the organism for over expression may be any microorganism having heterologously expressed PKS or part thereof.

More particularly the microorganism is selected from the genus Streptomyces. Particularly Streptomyces tsukubaensis, Streptomyces sp. ATCC 55098 or Streptomyces hygroscopicus var. ascomyceticus ATCC 14891 may be used.

Moreover, it is also contemplated to use the following microorganisms for carrying out the process of the present invention: Streptomyces tsukubaensis No. 9993 (Ferm BP-927), Streptomyces hygroscopicus subsp. hygroscopicus (DSM 40822), Streptomyces sp. AA6554, Streptomyces hygroscopicus var. ascomyceticus MA 6475 ATCC 14891, Streptomyces hygroscopicus var. ascomyceticus MA 6678 ATCC 55087, Streptomyces hygroscopicus var. ascomyceticus MA 6674, Streptomyces hygroscopicus var. ascomyceticus ATCC 55276, Streptomyces hygroscopicus subsp. ascomyceticus ATCC 14891, Streptomyces kanamyceticus KCC S-0433, Streptomyces clavuligerus CKD1119, Streptomyces hygroscopicus subsp. yakushimaensis, Streptomyces sp. DSM 7348, Micromonospora n.sp. A92-306401 DSM 8429, Streptomyces sp. MA 6548 and Streptomyces sp. MA 6858 ATCC 55098.

In one embodiment, this invention refers to the use of the second group of the genes which are not clustered at the specific FK506 gene cluster on the S. tsukubaensis chromosome. These genes are involved in the metabolism of butyryl-CoA and ethylmalonyl-CoA, a precursor for biosynthesis of ascomycin (FK520).

In order to reduce or abolish ethylmalonyl-CoA supply in S. tsukubaensis, several strategies were followed. In this respect, the invention relates to the use of nucleotide sequences of genes which are involved in the metabolism of ethylmalonyl-CoA, a building unit for ascomycin biosynthesis encoding the following enzymes:

    • a) crotonyl-CoA reductase (referred to as ccr respectively as ccr-gene hereinafter),
    • b) ethylmalonyl-CoA mutase (referred to as ecm respectively as ecm-gene hereinafter).

The nucleotide sequences and amino acid sequences are listed in the appendix (see SEQ.ID.#11, SEQ.ID.#12).

In this aspect the present application is directed to a process for the preparation of tacrolimus, wherein the process comprises the step of cultivation of a genetically modified strain of a microorganism, preferably of the genus Streptomyces, more preferably a genetically modified strain of Streptomyces tsukubaensis, wherein the genetic material of the microorganism comprises at least one inactivated and/or over expressed gene selected from crotonyl-CoA reductase (ccr) gene according to SEQ.ID.#11, and ethylmalonyl-CoA mutase (ecm) gene according to SEQ.ID.#12.

In particular the process for the preparation of tacrolimus comprises the step of cultivation of a genetically modified strain of a microorganism, preferably of the genus Streptomyces, more preferably a strain of Streptomyces tsukubaensis, wherein the genetic material of the microorganism comprises inactivated crotonyl-CoA reductase (ccr) gene according to SEQ.ID.#11.

In particular the process for the preparation of tacrolimus comprises the step of cultivation of a genetically modified strain of a microorganism, preferably of the genus Streptomyces, more preferably a strain of Streptomyces tsukubaensis, wherein the genetic material of the microorganism comprises over expressed ethylmalonyl-CoA mutase (ecm) gene according to SEQ.ID.#12.

This improved process for the preparation of tacrolimus exhibits significantly reduced or abolished production of ascomycin (FK520), thus significantly simplifying the tacrolimus purification process.

Gene homologues of ccr and icm were identified in several organisms to be involved in the biosynthesis of butyryl-CoA and consequently ethylmalonyl-CoA. The coenzyme B12-dependent isobutyryl-CoA mutase (icm; butanoyl-CoA:2-methylpropanoyl-CoA mutase, EC 5.4.99.13) catalyzes the reversible rearrangement between isobutyryl-CoA and n-butyryl-CoA in a reaction closely related to the known methylmalonyl-CoA mutase (mcm) reaction. Crotonyl-CoA reductase (EC 1.3.1.38, acyl-CoA:NADP′ trans-2-oxidoreductase) catalyzes the conversion of crotonyl-CoA to butyryl-CoA, a key substrate for ethylmalonyl-CoA biosynthesis or, under some circumstances, directly converts crotonyl-CoA to ethylmalonyl-CoA. Gene homologues of ecm (ethylmalonyl-CoA mutase) have been shown to convert ethylmalonyl-CoA to methylsuccinyl-CoA thereby effectively altering the ratio of ethyl-substituted products in the mixture.

It is known that crotonyl-CoA reductase genes (ccr-gene) and ethylmalonyl-CoA mutase genes (ecm-genes) are involved in several metabolic and biosynthetic pathways in different microorganismen. The role of ecm and ccr in the polyketide biosynthesis, in particular in the biosynthesis of ethylmalonyl-CoA, have been described (e.g. the role of ecm in production of monensin in S. cinnamonensis, Zhang W. et al. 2001, J. Bacteriol; 183:2071-2080).

Therefore, the present invention describes a method of producing a microorganism having reduced intracellular level of ethylmalonyl-CoA. This is achieved by blocking enzymes involved in biosynthesis of ethylmalonyl-CoA and/or over expressing enzymes consuming ethylmalonyl-CoA.

The activity of crotonyl-CoA reductase (ccr) specifically involved in the biosynthesis of key building units for the biosynthesis of FK506/520 in Streptomyces tsukubaensis was modified. In addition, ethylmalonyl-CoA mutase (ecm), involved in further processing of ethylmalonyl-CoA, was over expressed in the tacrolimus producing strain Streptomyces tsukubaensis.

In one embodiment the present application is directed to a genetically modified strain of a microorganism, preferably belonging to the genus Streptomyces, more preferably a genetically modified strain of Streptomyces tsukubaensis, wherein the genetic material of the microorganism comprises at least one inactivated and/or over expressed gene selected from the group of

    • ccr gene according to SEQ.ID.#11, encoding crotonyl-CoA reductase, and
    • ecm gene according to SEQ.ID.#12, encoding ethylmalonyl-CoA mutase.

In a preferred embodiment the genetically modified strain of a microorganism as described in the present application is a double modified microorganism, which comprises two inactivated and/or over expressed genes as described in the present application. It was found, that double modified microorganism has substantially improved characteristics compared to wild type microorganism as well as single mutants.

The inactivation of crotonyl-CoA reductase gene homologue (ccr) and over expression of ethylmalonyl-CoA mutase (emc) lead to an improved process for production of tacrolimus, characterized by a significant reduction of ascomycin biosynthesis. It seems that under the tested growth conditions the mutase-catalyzed reaction proceeds from butyryl-CoA to isobutyryl-CoA. The ethylmalonyl-CoA mutase (ecm) gene was found to effectively consume ethylmalonyl-CoA when over expressed in the producing strain.

In one aspect, the invention provides a genetically modified microorganism, preferably of the genus Streptomyces, more preferably a strain of Streptomyces tsukubaensis, wherein the genetic material of the microorganism comprises inactivated crotonyl-CoA reductase gene (ccr) according to SEQ. ID. #11. The method of inactivating such gene in microorganism is well known in the art, for example as described in the handbook “Practical Streptomyces genetics” (Kieser et al., 2000, Practical Streptomyces genetics, A laboratory Manual. ISBN0-7084-0623-8).

In another aspect, the invention provides a genetically modified microorganism, preferably of the genus Streptomyces, more preferably a strain of Streptomyces tsukubaensis, wherein the genetic material of the microorganism comprises over expressed ethylmalonyl-CoA mutase gene (ecm) according to SEQ. ID. #12. The method of over expressing such gene in a microorganism is well known in the art, for example as described in the handbook “Practical Streptomyces genetics” (Kieser et al., 2000, Practical Streptomyces genetics, A laboratory Manual. ISBN0-7084-0623-8).

In a further aspect, the present invention provides a genetically modified microorganism, preferably of the genus Streptomyces, more preferably a strain of Streptomyces tsukubaensis, comprising inactivated crotonyl-CoA reductase gene (ccr) according to SEQ. ID. #11 and over expressed ethylmalonyl-CoA mutase (ecm) according to SEQ. ID. #12 as said above. In this aspect the use of double modified microorganism has substantially improved characteristics compared to wild type microorganism as well as single mutants described above.

In particular the invention relates to the following strains of Streptomyces tsukubaensis:

    • a) Streptomyces tsukubaensis F130
      • deposited with the deposition number DSM 22506 on 23 Apr. 2009, at the DSMZ—Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganism and Cell Cultures) in Braunschweig/Germany. This strain is described as NRRL 18488 Δccr:Ts.
    • b) Streptomyces tsukubaensis F879
      • deposited with the deposition number DSM 22510 on 23 Apr. 2009, at the DSMZ—Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganism and Cell Cultures) in Braunschweig/Germany. This strain is described as NRRL 18488 ecm+.

The newly developed strains exhibits markedly reduced ascomycin content representing a significant improvement of tacrolimus fermentative production.

Further provided by the invention is the above mentioned nucleotide sequence encoding gene involved in ethylmalonyl-CoA biosynthesis of an microorganism Streptomyces tsukubaensis NRRL 18488 comprising the ccr gene sequence according to SEQ. ID #11, the sequence encoding for crotonyl-CoA reductase (Ccr), having amino acid sequence according to SEQ. ID #23, and variants thereof comprising one or more nucleotide additions, deletions, substitutions or inversions. Also provided by the invention is the nucleotide sequence encoding gene involved in ethylmalonyl-CoA consumption of an microorganism Streptomyces tsukubaensis NRRL 18488 comprising the ecm gene sequence according to SEQ. ID #12, the sequence encoding for ethylmalonyl-CoA mutase (ecm), having amino acid sequence according to SEQ. ID #24, and variants thereof comprising one or more nucleotide additions, deletions, substitutions or inversions. Also, provided by the invention is a nucleotide sequence as described above wherein the nucleotide sequence have at least 50% identity, preferably at least 60% identity, preferably at least 70%, preferably at least 80%, preferably at least 90% with sequence according to SEQ. ID #11 and SEQ. ID #12.

The present invention provides an improved process for the preparation of tacrolimus, in particular an industrial fermentative process, wherein the process comprises the step of cultivation of a genetically modified strain of a microorganism, wherein the genetic material of the microorganism comprises at least one inactivated and/or over expressed gene involved in the metabolism and/or the biosynthesis of ethylmalonyl-CoA and/or allylmalonyl-CoA. The process can be carried out by using at least one of the genetically modified strains of a microorganism as described above. In the following this process is described in more detail:

In particular the process according to the present invention comprises the following steps:

Step a) Generation of Genetically Modified Strain of a Microorganism

Preferably the present process for the production of tacrolimus encompasses the step of genetically modification of microorganism strains as described by this invention. In this sense the invention specifically relates to a genetically modified strain of Streptomyces tsukubaensis wherein the genetic material of the strain comprises at least one inactivated and/or over expressed gene involved in the metabolism and/or biosynthesis of ethylmalonyl-CoA and/or allylmalonyl-CoA.

Procedures to generate Streptomyces tsukubaensis for further modification according to the present invention are known to the person skilled in the art. Moreover, suitable strains of Streptomyces tsukubaensis are commercially available. One specific, non-limiting example of a suitable strain is the wild type Streptomyces tsukubaensis having the deposit number NRRL 18488.

The method of inactivating gene in microorganism is well known in the art, for example as described in the handbook “Practical Streptomyces genetics” (Kieser et al., 2000, Practical Streptomyces genetics, A laboratory Manual. ISBN0-7084-0623-8).

In a preferred embodiment a preparation of spores respectively a concentrated spore suspension in a sporulation medium of genetically modified strain of microorganism preferably a stain of S. tsukubaensis is carried out.

Step b) Preparation of Seed Medium

Cultivation of the modified strains of Streptomyces tsukubaensis as described in the present invention can be carried out by methods known to a person skilled in art. Cultivation processes of Streptomyces tsukubaensis are for example described in the handbook “Practical Streptomyces genetics” (Kieser et al., 2000, Practical Streptomyces genetics, A laboratory Manual. ISBN0-7084-0623-8).

Preferably the production of seed microorganism which can be used in the main fermentation process for the production of tacrolimus starts from a spore form of said genetically modified microorganism. In this respect the process according to the present application comprises the preparation of spore stock of described genetically modified microorganism, preferably of Streptomyces tsukubaensis, and optionally a concentrated spore suspension of described genetically modified microorganism. This preparation of spore form may be carried out using method known in the state of art, such as using a sporulation medium comprising a salt of manganese. Preferably this spore stock or concentrated spore suspension of genetically modified strain of microorganism is used to produce a vegetative seed medium by inoculation to a vegetative medium. The production of vegetative form of described microorganism should prepare with inoculation of a relatively small quantity of seed medium with the spores.

The seed medium may be transferred aseptically to a bioreactor.

In principle the cultivating of seed microorganism can be carried out under the conditions (e.g. pH, and temperature) as in the main fermentation process (described under step c).

Step c) Main Fermentation Process

Preferably the main fermentation process using genetically modified microorganism as described in the present application is carried out in a bioreactor in particular under agitation and/or aeration. Preferably, the process for the production of tacrolimus as described in the present application is carried out under submerged aerobic conditions in aqueous nutrient medium (production medium), containing sources of assimilable carbon, nitrogen, phosphate and minerals. Isolation of tacrolimus, which was produced in the main fermentation process from the said medium, may be carried out in a further separation step (step d).

Preferably the main fermentation process comprises the inoculation of production medium with seed microorganism obtained in step b) in particular by aseptically transfer into the reactor. It is preferred to employ the vegetative form of the microorganism for inoculation.

The addition of nutrient medium (production medium) in the main fermentation process into the reactor can be carried out once or more batch-wise or in a continuous way. Addition of nutrient medium (production medium) can be carried out before and/or during the fermentation process.

The preferred sources of carbon in the nutrient media can selected from dextrin, glucose, soluble starch, glycerol, lactic acid, maltose, fructose, molasses and sucrose as exemplified below.

The preferred sources of nitrogen in the nutrient media are yeast extract, soy peptone, soybean meal, bacterial peptone, casein hydrolysate, L-lysine, ammonium sulphate, corn steep liquor and other.

Inorganic/mineral salts such as calcium carbonate, sodium chloride, sodium or potassium phosphate, magnesium, manganese, zinc, iron and other salts may also be added to the medium.

The main fermentation process by the present process is carried out at a pH in the range of about 6.3 to 8.5 and temperature in the range of 20 to 35° C. Preferably the pH is in the range of about 6.5 to 8.3 and the temperature is in the range of about 23 to 31° C.

Preferably, the production cultures are incubated for 80 to about 300 hours, more preferably for about 130 to 280 hours.

The production of tacrolimus could be performed in aerobic conditions with agitation and aeration of production medium. Agitation and aeration of the culture mixture may be accomplished in a variety of ways. The agitation of production medium may be provided by a propeller or similar mechanical device and varied to various extents according to fermentation conditions and scale. The aeration rate can be varied in the range of 1.0 to 2.5 VVM (gas volume flow per unit of liquid volume per minute (volume per volume per minute)) with respect to the working volume of the bioreactor.

Further known additives for fermentative process may be added in particular in the main fermentation process. To prevent excessively foaming of the culture medium anti-foaming agents could be added, such as silicone oil, fatty oil, plant oil and the like. Particularly a silicone-based anti-foaming agent may be added during the fermentation process to prevent excessively foaming of the culture medium.

Step d) Separation and Purification of Product from the Fermentation Broth (Harvest)

Tacrolimus from the fermentation broth can be separated and purified by conventional methods commonly used for recovery of biologically active substances. The produced tacrolimus can be recovered from the fermentation broth by extraction in organic solvent i.e. acetone, ethanol or methanol.

Optionally the extract may be then concentrated, column chromatographed with XAD16 adsorber using acetone: water mixture to get crude tacrolimus. The crude substance may be further purified on preparative HPLC to get pure tacrolimus.

A preferred embodiment of process steps according to the present application can be summarized as follows:

    • i) Preparation of the S. tsukubaensis spore stocks from the said strains by cultivating said strains on the solid sporulation agar medium at 28° C. for 10 to 14 days.
    • ii) Spores of the S. tsukubaensis strains were harvested to produce concentrated spore suspension and inoculation to the 600 mL of vegetative medium and incubate on the shaker at 220 rpm for 24-32 hours until PMV 10-20% of vegetative medium is reached. pH at the harvest time is in the range of 6.8 to 7.3.
    • iii) Propagation of seed vegetative inoculum to the desired volume of 10% in order to inoculate production medium. 10 liter fermenter containing of vegetative medium is inoculated with vegetative seed and cultivated for 24 to 28 hours at 28° C.
    • iv) 10% of the vegetative seed culture is used to inoculate 100 L of the production medium. Fermentation process is carried out for 120 to 180 hours at 28° C. and pH maintained at 7.0-7.2 using sulphuric acid or sodium hydroxide solution.

In the following as a non limiting example preferred media for sporulation, seed growth and main fermentative process are described:

    • 1) Solid agar sporulation medium (ISP4) comprised of soluble starch (10 g/L), sodium chloride (1 g/l), ammonium sulphate (2 g/L), calcium carbonate (2 g/L), K2HPO4 (1 g/l), MgSO4×7H2O (1 g/L), FeSO4×7H2O (0.001 g/L), MnCl2×4H2O (0.001 g/L), ZnSO4×7H2O (0.001 g/L) and bacteriogical agar (20 g/L). The pH should be adjusted to 7.0±0.2 prior to sterilization by suitable addition of base or acid.
    • 2) Seed medium comprised of soybean meal (2.5 g/L), dextrin (10 g/L), glucose (1 g/L), yeast extract (5 g/L), casein hydrolizate (7 g/L), K2HPO4 (0.2 g/L), NaCl (0.5 g/L), MnCl2×4H2O (0.005 g/L), FeSO4×7H2O (0.025 g/L), ZnSO4×7H2O (0.001 g/L), MgSO4×7H2O (0.005 g/L) and CaCl2 (0.02 g/L). The pH should be adjusted to 7.0±0.2 prior to sterilization by suitable addition of base or acid.
    • 3) Production medium containing dextrin (60-120 g/L), glucose (0-15 g/L), soybean meal (5-20 g/L), soya peptone (5-20 g/L), glycerol (5-20 g/L), L-lysine (1-7.5 g/L), K2HPO4 (0.5-2 g/L), CaCO3 (1-5 g/L) and polyethylene glycol (1-5 g/L). The pH should be adjusted to 7.0±0.2 prior to sterilization by suitable addition of base or acid.

In another preferred embodiment of the invention the main fermentation process (step c) is carried out under external addition of allylmalonyl-CoA or at least one precursor (analogue) of allylmalonyl-CoA. In terms of the present invention allylmalonyl-CoA precursors also includes analogues of allylmalonyl-CoA.

In this respect, the present invention provides a process for the preparation of tacrolimus, in particular an industrial fermentative process, wherein the process comprises the step of cultivation of a genetically modified strain of a microorganism belonging to the genus Streptomyces, wherein the genetic material of the microorganism comprises at least one inactivated and/or over expressed gene involved in the metabolism and/or the biosynthesis of ethylmalonyl-CoA and/or allylmalonyl-CoA and wherein the process is carried out under the external addition of allylmalonyl-CoA and/or at least one precursor (analogue) of allylmalonyl-CoA.

In particular the invention is directed to a fermentative preparation of tacrolimus (or related compounds) by cultivating a genetically modified strain of S. tsukubaensis, wherein the biosynthetic pathway(s) providing allylmalonyl- and etlhylmalonyl CoA-activated precursors is inactivated, for example by inactivation of AIIR gene, and adding or feeding in controlled manner allylmalonyl-CoA or ethylmalonyl-CoA SNAC precursors into the culture medium during the fermentation process. This results in the production of tacrolimus or ascomycin compounds in the significant amounts compared to the wild-type strain. Thus, the novel process described herein resulted in process in which tacrolimus or ascomycin are produced exclusively, this way significantly simplifying the downstream process.

The fermentation process for the production of pure tacrolimus or pure ascomycin under external addition of allylmalonyl-CoA or ethylmalonyl-CoA or at least one precursors (analogues) thereof described herein using genetically modified strains of a microorganism belonging to genus Streptomyces, in particular a genetically modified strain of S. tsukubaensis, may be carried out under submerged aerobic conditions in aqueous nutrient medium, containing sources of assimilable carbon and nitrogen similar as described earlier.

Preferably, the target concentration range of the allylmalonyl or ethylmalonyl ester precursors is in the range of 0.1 to 5.0 g/L and more preferably in the range of 0.5 to 3.0 g/L. The target concentration may be recorded on a tangible data storage medium, preferably before the commencement of the fermentation process. For the feeding process different allylmalonyl or ethylmalonyl ester precursors could be used. Allylmalonyl or ethylmalonyl N-acetyl cysteamine (SNAC) thioesters are preferred. Both, single or double thioesters, or mixtures thereof can be used.

Tacrolimus from the fermentation broth can be separated and purified by conventional methods commonly used for recovery of biologically active substances. The process thus has significant cost advantages compared to classic process where preparative HPLC has to be employed in the downstream process.

Furthermore, the present invention deals with the use of genetically modified strain of Streptomyces tsukubaensis as described above in a process for the fermentative production of tacrolimus.

In a further aspect, the present invention relates to a pharmaceutical composition comprising tacrolimus or a pharmaceutically acceptable derivative or analog thereof produced by cultivation of a genetically modified strain of Streptomyces tsukubaensis as described above. The term “analog” or “derivative” is used herein in the conventional pharmaceutical sense, to refer to a molecule that structurally resembles a reference molecule, but has been modified in a targeted and controlled manner to replace one or more specific substituents of the referent molecule with an alternate substituent, thereby generating a molecule which is structurally similar to the reference molecule. In addition, using methods known to those skilled in the art, analogs and derivatives of the compound tacrolimus can be created which have improved therapeutic efficacy, i.e., higher potency and/or selectivity at a specific targeted receptor type, either greater or lower ability to penetrate mammalian blood-brain barriers (e.g., either higher or lower blood-brain barrier permeation rate), fewer side effects, etc.

The phrase “pharmaceutically acceptable”, as used in connection with compositions of the invention, refers to molecular entities and other ingredients of such compositions that are physiologically tolerable and do not typically produce untoward reactions when administered to a mammal, e.g., a human. Preferably, as used herein, the term “pharmaceutically acceptable” means approved by a regulatory agency of the Federal or a state government or listed e.g. in the U.S. Pharmacopeia or other generally recognized pharmacopoeia for use in mammals, and more particularly in humans.

A further embodiment of the invention is a pharmaceutical composition comprising at least one compound of formula (I) or a polymorphic form thereof or a pharmaceutically acceptable salt thereof and at least one further pharmaceutically tolerable additive. The pharmaceutical composition can also comprise a further drug compound. In the pharmaceutical compositions of the present invention, the compounds of formula (I), in particular tacrolimus, or a polymorphic form or pharmaceutically acceptable salt thereof is formulated as dosage units containing e.g. from 0.1 to 4000 mg, preferably 1 to 2000 mg, of said compound or a pharmaceutically acceptable salt thereof per dosage unit for daily administration. For all aspects of the invention, particularly medical ones, the administration of a compound or composition has a dosage regime which will ultimately be determined by the attending physician and will take into consideration such factors such as the compound being used, animal type, gender, age, weight, severity of symptoms, method of administration, adverse reactions and/or other contraindications. Specific defined dosage ranges can be determined by standard design clinical trials with patient progress and recovery being fully monitored. Such trials may use an escalating dose design using a low percentage of the maximum tolerated dose in animals as the starting dose in man.

The physiologically acceptable compound according to the invention will normally be administered in a daily dosage regimen (for an adult patient) of, for example, an oral dose of between 0.01 mg/kg (mg per kilogram of body weight of the mammal to be treated) and 100 mg/kg, preferably between 0.1 mg/kg and 75 mg/kg.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows the genetic organisation of “All-gene”-subcluster (15080 bp) of Streptomyces tsukubaensis.

FIG. 2 shows LC-MS chromatograms (MRM) for monitoring the presence of tacrolimus and ascomycin in extracted fermentation broths of Streptomyces hygroscopicus var. ascomyceticus ATCC 14891. Ascomycin is produced by the wild type strain (row 2) and a mutant strain overexpressing the aIIA, aIIK, aIIR and aIID genes (row 4). On the other hand, tacrolimus is not produced by the wild type strain (row 1) and is only produced when the aIIA, aIIK, aIIR and aIID are overexpressed (row 3).

The SEQ-ID # and the gene function are given in table 2:

TABLE 2 SEQ. ID. # Gene Name Gene Function 2. AllA Acyltransferase and acyl-Carrier Protein 3. AllK Ketoacyl synthase 4. AllR Enoyl CoA reductase 5. AllD Acyl-CoA dehydrogenase 6. AllM Methionine gamma lyase 7. AllN Transcriptional regulator 8. AllP P450 monooxygenase 9. AllO Acyl-CoA oxidoreductase 10. AllS Acetoacetyl-CoA reductase

The following examples are for illustrating the present invention.

EXPERIMENTAL PROCEDURES

The following are detailed examples of the experimental procedures used to clone and analyse “ccr”, “AIIK”, “AIIR”, “AIIP” and “ecm” genes, and for the generation of Streptomyces tsukubaensis mutants using these gene homologues. Also included are examples of fermentation procedures using these strains and determinations of FK506 and FK520 production yields. Additional details of standard techniques, which are well known to those skilled in molecular biology or microbiology, and the designation of the particular enzymes used, are described, for example, in the handbook “Practical Streptomyces genetics” (Kieser et al., 2000, Practical Streptomyces genetics, A laboratory Manual. ISBN0-7084-0623-8).

Example 1 Maintenance and Spores Preparation of Streptomyces tsukubaensis Strains

Streptomyces tsukubaensis strains mycelium were grown as a confluent lawn on the sporulation medium ISP4 for 8-14 days at 28° C. The ISP4 medium comprised:

Soluble starch 10 grams K2HPO4 1 gram MgSO4 × 7 H2O 1 gram NaCl 1 gram (NH4)2SO4 2 grams CaCO3 2 grams FeSO4 × 7 H2O 0.001 gram MnCl2 × 4 H2O 0.001 gram ZnSO4 × 7 H2O 0.001 gram Bacteriological agar 20 grams Final volume 1 liter pH adjusted to 7.0

The pH was adjusted to 7.0 with 1 M NaOH. Sterilization was performed at 121±2° C., 120±10 kPa for 20 minutes. After 8-14 days of growth, spores were collected and stored at −20° C. in glycerol (20%) until use.

Example 2 Preparation of Streptomyces tsukubaensis Genomic DNA

Spores of Streptomyces tsukubaensis NRRL 18488 (wild type) were used to inoculate 50 ml of TSB medium (Kieser et al., 2000, Practical Streptomyces genetics, A laboratory Manual. ISBN-0-7084-0623-8) in a 250-ml Erlenmeyer flask, which was maintained with shaking (210 rpm) at 28° C. for 24 hours. Cultures were grown for 24 hours at 28° C. Mycelium was recovered by centrifugation and genomic DNA was prepared using PureLink Genomic DNA Mini Kit (Invitrogen) according to the instructions of the kit manufacturer. DNA was resuspended in 100 μl TE buffer (Sambrook, and Russell, 2000, Molecular Cloning: A Laboratory Manual, ISBN-978-087969577-4).

Example 3

The isolated Genomic DNA was sequenced with Roche FLX technology at GATC AG, Germany. Once the sequence contigs belonging to the FK506 biosynthesis genetic cluster were identified the position and orientation of open reading frames (ORFs) was analyzed using the FramePlot beta 4.0. Software (Ishikawa et al., FEMS Microbiot Lett 174 (1999) 251-253). Using the predicted amino acid sequences, homology searches were carried out in GenBank databases using BLASTp and BLASTx algorithm at the NCBI (NCBI/Blast: http://blast.ncbi.nlm.nih.gov/Blast.cgi). Based on these results and supported by conserved domain searches, putative gene functions were assigned.

In total 15 ORFs were identified to the left from fkbC. Six of these show high similarity with the ORFs present in the FK520 cluster (fkbL—lysine cyclodeaminase, fkbG, fkbH, fkbI, fkbJ, fkbK—five genes involved in methoxymalonyl-ACP biosynthesis) and nine genes were predicted to form the “allyl subcluster”. This subcluster consists of 1 gene containing acyltransferase and acyl carrier protein domains, 1 gene containg a ketoacyl synthase domain, 1 distant crotonyl-CoA reductase domain, 2 distant acyl-CoA dehydrogenase domain containing homologues, 1 methionine gamma lyase containing gene, 1 AsnC family regulator gene, 1 P450 monooxygenase gene and 1 distant acetoacetyl-CoA reductase homologue.

Example 4 Construction of Vectors for Disruption of the Ccr Gene, Construction of Mutant Strains of S. Tsukubaensis NRRL 18488 with Inactivated Ccr Gene and Analysis of Tacrolimus and Ascomycin Production of the Said Mutants

    • a) Design of primers: Primers for amplification of a large region of ccr gene were designed based on conserved regions of other known ccr genes of different Streptomyces species, found using BLAST search with ccr gene from Streptomyces coelicolor (Protein ID: NP—630556.1, GeneID:1101912) as template, and a ClustalW pile-up sequence comparison of the obtained BLAST results. Thus, ccr-F2 (GTCTAGACCACATCATCGGCTCCGACC) (SEQ ID NO: 22) with an XbaI restriction site and ccr-R1 (CGAATTCACGCCGACCTTGCCCTGGTGC) (SEQ ID NO: 23) with an EcoRI restriction site were made to amplify a 917 bp long region of ccr gene.
    • b) PCR amplification of DNA fragments: S. tsukubaensis genomic DNA obtained in Example 2 was PCR amplified using a Biorad iCycler Thermal Cycler. The PCR reaction was carried out with Pfu polymerase (New England Biolabs) and the buffer provided by the manufacturer in the presence of 200 μM dNTP, 10% glycerol, 0.5 μM of each primer, approximately 50 ng of template S. tsukubaensis genomic DNA and 2.5 units of enzyme in a final volume of 100 μl for 30 cycles. The thermal profile of all 30 cycles was 95° C. for 45 sec (denaturation step), 69° C. for 45 sec (annealing step), and 72° C. for 1 min (extension step). The PCR-amplified product was cloned into a pUC19 cloning vector. The sequence analysis of the cloned PCR product confirmed its respective partial ccr sequence.
    • c) Construction of a temperature-sensitive pKC1139-based and suicide pKC1132-based vectors to be used in the disruption of the S. tsukubaensis ccr gene by homologous recombination: The F2-R1 amplified fragment of ccr gene was excised from pUC19 by EcoRI and XbaI restriction sites and the transferred by ligation into vectors pKC1139 and pKC1132 which were previously cut with EcoRI and XbaI restriction enzymes, making pKC1139-ccr and pKC1132-ccr. Vector pKC1139 contains a normal pUC19-based Ori for replication in E. coli, but a temperature-sensitive Ori for replication in Streptomyces, which is unable to function at elevated temperatures above 34° C. (Bierman et al., 1992 Gene. 116(1):43-9, Muth et al., 1989 Mol Gen Genet. 219(3): 341-348). Vector pKC1132 only contains the normal pUC19-based Ori for replication in E. coli but cannot maintain replication in Streptomyces (Bierman et al., 1992 Gene. 116(1):43-9) and is, thus, lost without integration into genome by homologous recombination. Vectors pKC1139-ccr1 and pKC1132-ccr were then opened using BamHI restriction enzyme which cuts within the ccr gene, splitting the 917 bp long fragment into 346 bp on one side and 571 bp on the other side, which were then blunt-ended with DNA Polymerase I, Large (Klenow) Fragment. A cassette, conferring thiostrepton (Ts) resistance, was then introduced into pKC1139-ccr and pKC1132-ccr BamHI-cut and blunt-ended vectors. The p330 vector was digested with XbaI restriction enzyme, the approximately 961 bp long fragment containing the Ts cassette was blunt-ended with DNA Polymerase I, Large (Klenow) Fragment and ligated into the pKC1139-ccr and pKC1132-ccr vectors, making pKC1139-ccrTs and pKC1132-ccrTs vectors, respectively.
    • d) Introduction of vectors for disruption of the ccr gene into the S. tsukubaensis NRRL 18488 strain: Plasmid constructs pKC1139-ccrTs and pKC1132-ccrTs were introduced by transformation into electrocompetent E. coli strain ET12567 containing the conjugative plasmid pUZ8002 (Paget et al., 1999 J. Bacteriol. 181: 204-211). The plasmid pUZ8002 contains all the necessary genes for construction of conjugative pilli, however it lacks the origin of transfer and, thus, remains in the host cell (Jones et al., 1997 Mol. Microbiol. 23:169-178). Conjugation procedure was done as described in Kieser et al., 2000 (Practical Streptomyces genetics, A laboratory Manual. ISBN0-7084-0623-8). Only transformation with vector pKC1139-ccrTs gave exconjugants. Exconjugants were grown at 28° C. on Sporulation medium which is described in Example 1 with addition of 50 μg/ml apramycin.
    • e) Selection for stable secondary recombinant strains of S. tsukubaensis with disrupted ccr gene by thiostrepton resistance conferring cassette: S. tsukubaensis exconjugants of vector pKC1139-ccrTs, grown at 28° C. on Sporulation medium with addition of 50 μg/ml apramycin were inoculated into liquid TSB medium with thiostrepton (25 μg/ml) and grown in shake flasks at 28° C. and 210 rpm without the addition of apramycin to produce good seed culture. After 24 h, seed culture was subcultivated into a new shake flask with fresh TSB medium with thiostrepton (25 μg/ml) and grown at an increased temperature, higher than 24° C. and 210 rpm. Above 34° C. the pKC1139-based vector is unable to replicate and is forced to integrate into the S. tsukubaensis genome, thus yielding primary recombinants. The culture was further subcultivated several times into new shake flasks with fresh TSB medium with thiostrepton (25 μg/ml), and then plated onto Sporulation medium with thiostrepton and grown at 28° C. Harvested spores were filtered and serial dilution was made on plates of Sporulation medium. After 5-8 days single colonies were patched onto plates with Sporulation medium with thiostrepton, and on plates of Sporulation medium with thiostrepton and apramycin. Primary recombinants are still resistant to apramycin, while secondary recombinants lost the apramycin resistance and cannot grow on Sporulation medium with apramycin. Selected secondary recombinant strains were also confirmed by Southern hybridization as described in next paragraph.
    • f) Analysis of S. tsukubaensis ccr-disrupted mutants genomic DNA by Southern Hybridization: Preparation of DIG-labelled plasmid DNA probe: Only the insert (part of the ccr gene with inserted TsR cassette) of the plasmid pKC1139-ccrTs was used as a probe; the vector was digested with EcoRI and XbaI restriction enzymes and the 1.744 bp long fragment purified with a Wizard SV Gel and PCR Clean-Up System (Promega). Approximately 1 μg of the eluted fragment was labelled over-night with digoxigenin-dUTP by random primed labelling technique using the DIG High Prime DNA Labelling and Detection Starter Kit I (Roche).
      • i) DNA transfer: Genomic DNA of S. tsukubaensis wild type and pKC1139-ccrTs mutants (putative primary recombinants and secondary recombinants) was prepared using the PureLink Genomic DNA Mini Kit (Invitrogen) according to the instructions of the kit manufacturer. Approximately 10 μg of each isolated genomic DNA was digested with NaeI restriction enzyme. At the end of the digestion, the DNA fragments were separated by electrophoresis in a 1% agarose gel at 20 V for 12 hours, and transferred to a positively charged Hybond-N+ nylon membrane (GE Healthcare) using the alkali capillary blotting method (Southern, E. M., 1975, J. Mol. Biol., 98:503) for 6 hours.
      • ii) Hybridisation: Pre-hybridization and hybridization of DIG-labeled DNA probe to DNA immobilized on a nylon membrane was performed as suggested by the DIG High Prime DNA Labeling and Detection Starter Kit I manufacturer (Roche). Pre-hybridization was carried out in the supplied pre-hybridization solution for 1 hour at 50° C. For hybridization, 1 μg of denatured DNA (at 90° C. for 10 minutes) was added to fresh pre-hybridization solution pre-warmed to 50° C. After overnight hybridization, membranes were washed as follows: two washes with 2×SSC, 0.1% SDS, at room temperature for 5 minutes, and two washes with 0.5×SSC, 0.1% SDS at 55° C. for 15 minutes.
      • iii) Immunological detection: The hybridized probes were immunodetected with anti-digoxigenin-AP Fab fragments and visualized with the colorimetric substrates NBT/BCIP, as suggested by the DIG High Prime DNA Labeling and Detection Starter Kit I supplier (Roche).
      • iv) Analysing the expected bands, true secondary recombinants derived by pKC1139-ccrTs vector were confirmed by described Southern hybridization procedure. The ccr-disrupted strain S. tsukubaensis F130 was selected for further testing on tacrolimus and ascomycin production.
    • g) Fermentative tacrolimus production of thiostrepton resistant ccr disrupted mutants derived by secondary homologous recombination using pKC1139-ccrTs.
      • i) Seed culture Process: Seed medium comprised:

Soy meal 2.5 grams Dextrin 10 grams Glucose 1 gram Yeast extract 5 grams Casein hydrolyzate 7 grams K2HPO4 0.2 gram NaCl 0.5 gram MnCl2 × 4H2O 0.005 gram FeSO4 × 7H2O 0.025 gram ZnSO4 × 7H2O 0.001 gram MgSO4 × 7H2O 0.005 gram CaCl2 0.02 gram Final volume 1 liter
      •  The pH was adjusted to 7.0 with 1 M NaOH. 50 ml of this medium without glucose was filled into a 250 ml Erlenmeyer flask, closed with a foam plug and sterilized. Sterilization was performed at 121±2° C., 120±10 kPa for 25 minutes. After sterilization sterile glucose suspension was added. The sterilized Seed medium 50 μg/ml thiostrepton was added and spores of Streptomyces tsukubaensis strains (1% v/v) were inoculated in seed medium and incubated on shaker at 28° C. and 250 rpm for 24-48 hours under aerobic conditions.
      • ii) Main Fermentation Process: About 10% v/v of the above seed culture was used for the inoculation of a 250 ml Erlenmeyer flask, which contained 50 ml of Fermentation medium. The Fermentation medium contained:

Dextrin 90 grams Glucose 5 grams Soy meal 10 grams Soy peptone 10 grams Glycerol 10 grams L-lysine 2.5 gram K2HPO4 1 gram CaCO3 1.5 grams PEG (1000) 1 gram Final volume 1 liter
      •  The pH of the Fermentation medium was adjusted before sterilization to pH 7.0 with 1M NaOH. Sterilization was performed at 121° C. for 25 minutes. Fermentation was carried out on shaker at 28° C., 250 rpm for 6-7 days.
    • h) Determination of tacrolimus and ascomycin production with HPLC of thiostrepton resistant ccr disrupted mutants derived by secondary homologous recombination using pKC1139-ccrTs.:

Method for tacrolimus and ascomycin determination: The analysis for determination of tacrolimus or ascomycin production thereof was carried out by isocratic reversed phase HPLC using an appropriate column and running conditions: column Nucleosil-100 C18 (150×4.0 mm, particle size 3 μm), flow 1.5 ml/min, T° C.=60° C., mobile phase: 560 ml water, 335 ml acetonitrile, 70 ml MTBE and 0.2 ml 85% H3PO4, detection 210 nm, sample injection 20 μl.

The tacrolimus and ascomycin content in samples quantification was performed by using external standards of tacrolimus and ascomycin, where tacrolimus was eluted at 12.5 min and ascomycin at 11.5 min. Results are expressed as % of ascomycin production compared to tacrolimus production in samples.

Sample preparation: To 5 ml of well shaken broth 5 ml of methanol was added and samples were placed on a shaker for 1 hour to extract samples. After extraction, 1 ml of methanol extract of broth was taken to 1.5 ml tube and centrifuged for 10 min at 14000 rpm. 0.8 ml of supernatant was transferred into vials and to perform HPLC analysis.

% of ascomycin Tacrolimus production compared to Description of strain production (mg/l) tacrolimus production NRRL 18488 (w.t.) 43.4 ± 7.4  10.1 ± 1.6 Δccr Tsa 33.5 ± 13.4  6.4 ± 1.0 aSecondary recombinant mutants with disrupted ccr gene by integrated thiostrepton cassette. Mutants derived by secondary homologous recombination using pKC1139-ccrTs.

Isolated secondary recombinant mutants with disrupted ccr gene showed in average 40% reduction of ascomycin production compared to the wild type strain Streptomyces tsukubaensis NRRL 18488.

Example 5 Construction of Vectors for Disruption of the AIIR Gene, Construction of Mutant Strains of S. tsukubaensis NRRL 18488 with Inactivated AIIR and Analysis of Tacrolimus and Ascomycin Production of the Said Mutants

    • a) Design of primers: As described in Example 4, a 454-based whole genome sequencing was used on the genome of S. tsukubaensis, which allowed us to design primers for amplification of the regions flanking the AIIR gene, based on a known DNA sequence of the region flanking the AIIR gene. Thus, AIIR-F1 (CAAGCTTCACCGGTCCCGGGCTC) (SEQ ID NO: 24) with a HindIII restriction site and AIIR-R1 (GCATATGGTCCGGTTCGGGGGTGGG) (SEQ ID NO: 25) with an NdeI restriction site were made to amplify the upstream region of the AIIR gene, and AIIR-F2 (GGGTCACATATGGCGAACTACCGGG) (SEQ ID NO: 26) with an NdeI and AIIR-R2 (CGAATTCTGTGGGCCGACCTCACCCA) (SEQ ID NO: 27) with an EcoRI restriction site were made to amplify the downstream region of AIIR gene. Between primers AIIR-R1 and AIIR-F2, an 894 bp (298 amino acid) gap was generated for the deletion of almost entire 1335 bp AIIR gene. When the two overlapping fragments are combined at NdeI restriction site, the reading frame is preserved, which allows for an “in-frame” deletion of the target AIIR gene with a minimum impact on the downstream genes.
    • b) PCR amplification of DNA fragments: S. tsukubaensis genomic DNA obtained in Example 2 was PCR amplified using a Biorad iCycler Thermal Cycler using the same conditions as described in the paragraph ii of Example 4, using AIIR-F1+AIIR-R1 and AIIR-F2+AIIR-R2 primer combinations. The PCR-amplified products were cloned into a pUC19 cloning vector, and the sequence analysis of cloned PCR products confirmed their respective DNA sequence.
    • c) Construction of a temperature-sensitive pKC1139-based and suicide pKC1132-based vectors to be used in the disruption of the S. tsukubaensis AIIR gene by homologous recombination: The F1-R1 and F2-R2 amplified fragments of the flanking regions of the AIIR gene were excised from pUC19 by restriction enzymes HindIII and NdeI, and EcoRI and NdeI, respectively. Vectors pKC1139 and pKC1132 were previously cut with EcoRI and HindIII restriction enzymes, and the two fragments were combined and ligated into each of the target vector, making pKC1139-AIIR and pKC1132-AIIR, respectively. Vectors pKC1139-AIIR and pKC1132-AIIR were then opened using NdeI restriction enzyme, as described in paragraph iv of Example 4, and antibiotic resistance conferring cassette was inserted. For AIIR, different cassettes were used; thiostrepton (Ts) resistance cassette was obtained from the p330 vector as described in Example 4, erythromycin (Er) resistance cassette was obtained from pIJ4026 vector by digesting the vector with EcoRI and XbaI and blunt-ending the 1690 bp long fragment, and kanamycin (Kn) resistance cassette was obtained from pSuperCos1 (REFI) vector by digesting the vector with SmaI and HindIII and blunt-ending the 1323 bp long fragment. Each of the cassettes was ligated into the open pKC1132-AIIR and pKC1139-AIIR vectors, making pKC1132-AIIRTs, pKC1132-AIIREr, pKC1132-AIIRKn, pKC1139-AIIRTs, pKC1139-AIIREr, and pKC1139-AIIRKn vectors, respectively.
    • d) Introduction of vectors for disruption of the AIIR gene into the S. tsukubaensis NRRL 18488 strain: Plasmid constructs pKC1139-AIIRTs, pKC1139-AIIREr, and pKC1139-AIIRKn were introduced into S. tsukubaensis NRRL 18488 strain by the same conjugation procedure as described in Example 4d.
    • e) Selection for stable secondary recombinant strains of S. tsukubaensis with disrupted AIIR gene by antibiotic resistance conferring cassette: The procedure for selecting stable secondary recombinant strains of S. tsukubaensis with disrupted AIIR gene by thiostrepton antibiotic conferring cassette for S. tsukubaensis exconjugants of vectors pKC1139-AIIRTs, pKC1139-AIIREr and pKC1139-AIIRKn pKC1139-ccrTs was the same as described in Example 6. Subcultivation was carried out in liquid TSB medium with the corresponding antibiotic for which the resistance cassette is inserted between the flanking regions of the AIIR gene. Selected secondary recombinant strains were no longer able to grow on apramycin, but were able to grow on the secondary antibiotic for which the resistance cassette is inserted between the flanking regions of the AIIR gene.
    • f) Introduction of vectors for disruption of the AIIR gene into the S. tsukubaensis F130 strain already conferring inactivated ccr-gene: Plasmid pKC1139-AIIREr and pKC1139-AIIRKn were introduced into S. tsukubaensis F130 ccr-disrupted strain, described in Example 4, by the same conjugation procedure as described in Example 4d.
    • g) Selection for stable secondary recombinant strains of S. tsukubaensis with disrupted ccr gene by thiostrepton resistance conferring cassette and disrupted AIIR gene by erythromycin resistance conferring cassette: The procedure for selecting stable secondary recombinant strains of S. tsukubaensis, derivatives of S. tsukubaensis F130, with disrupted both ccr as well as AIIR genes was the same as described in Example 4e. Subcultivation was carried out in liquid TSB medium with the corresponding antibiotic for which the resistance cassette is inserted between the flanking regions of the AIIR gene. Selected secondary recombinant strains were no longer able to grow on apramycin, but were able to grow both thiostrepton (disrupting the ccr gene) as well as on the secondary antibiotic for which the resistance cassette is inserted between the flanking regions of the AIIR gene.
    • h) Fermentative tacrolimus production of erythromycin resistant AIIR disrupted mutants derived by secondary homologous recombination using pKC1139-AIIREr: Tacrolimus production for erythromycin resistant AIIR disrupted mutants was performed as described in Example 4g, except erythromycin 50 μg/ml was added to the Fermentation medium at the start of cultivation.
    • i) Fermentative tacrolimus production with double, ccr and AIIR disrupted mutants: Tacrolimus production for erythromycin resistant ccr and AIIR disrupted mutants was carried out as described in Example 4g, except thiostrepton and erythromycin ware added at the concentration of 50 μg/ml, each, to the fermentation medium at the start of cultivation. For the feeding experiments, allymalonyl-CoA and ethylmalonyl-CoA precursors, diethyl allylmalonyl-SNAC, allylmalonyl-di-SNAC and ethylmalonyl-SNAC, were added to the Fermentation medium in at 5-20 mM concentration.
    • j) Determination of tacrolimus and ascomycin production with HPLC of erythromycin resistant AIIR disrupted mutants derived by secondary recombination using pKC1139-AIIREr:

For the determination of tacrolimus and ascomycin production of erythromycin resistant AIIR disrupted mutants was used the same method as described in Example 4h.

Tacrolimus Ascomycin Dihydrotacrolimus production production production Description of strain (mg/l) (mg/l) (mg/l) NRRL 18488 (w.t.) 30.0 ± 6.6   3.2 ± 0.6 <1.0 ΔallR Era 0.0 0.0 0.0 ΔallR Era + 8.1 ± 2.3 0.0 0.0 allylmalonyl-SNAC ΔallR Era + 7.5 ± 2.0 0.0 0.0 allylmalonyl-diSNAC ΔallR Era + 0.0 10.2 ± 3.2 0.0 ethylmalonyl-CoA precursor aSecondary recombinant mutants with disrupted allR gene by integrated erythromycin cassette. Mutants derived by secondary homologous recombination using pKC1139-allREr.

Isolated secondary recombinant mutants with disrupted AIIR gene caused complete abolishment of tacrolimus production. When allylmalonyl-SNAC or alllymalonyl-diSNAC were added to the Fermentation medium, production of tacroliomus was re-established. Similarly, when ethylmalonyl-SNAC was added, ascomycin production was re-established.

    • k) Determination of tacrolimus and ascomycin production with HPLC of double, ccr and AIIR disrupted mutants:

For the determination of tacrolimus and ascomycin production of double, ccr and AIIR disrupted mutants, method as described in Example 4h was used.

Tacrolimus Ascomycin Dihydrotacrolimus production production production Description of strain (mg/l) (mg/l) (mg/l) NRRL 18488 (w.t.) 36.9 ± 9.9   3.5 ± 1.2 <1.0 Δccr allRa 0.0 0.0 0.0 Δccr allRa + 7.8 ± 2.0 0.0 0.0 allylmalonyl- CoA precursor Δccr allRa + 6.9 ± 2.2 0.0 0.0 allylmalonyl- CoA precursor Δccr allRa + 0.0 11.8 ± 2.1 0.0 ethylmalonyl- CoA precursor aSecondary recombinant mutants with disrupted ccr and allR genes by integrated erythromycin cassette. Mutants derived by secondary homologous recombination using pKC1139-allREr.

Complete abolishment of tacrolimus occurred with isolated secondary recombinant mutants with inactivated ccr and AIIR genes. When allylmalonyl-SNAC or allymalonyl-diSNAC were added to the Fermentation medium, production of tacroliomus was re-established. Similarly, when ethylmalonyl-SNAC was added, ascomycin production was re-established.

Example 6 Construction of Vectors for Disruption of the aIIK Gene, Construction of Mutant Strains of S. tsukubaensis NRRL 18488 with Inactivated aIIK and Analysis of Tacrolimus and Ascomycin Production of the Said Mutants

    • a) Design of primers: a 454-based whole genome sequencing was used on the genome of S.

tsukubaensis, which allowed us to design primers for amplification of the regions flanking the aIIK gene, based on the known DNA sequence of the region flanking the aIIK gene. Thus, aIIK-F1 (AGAATTCGTTACGGGGAGACGGCATCCCGG) (SEQ ID NO: 28) with an EcoRI restriction site and aIIK-R1 (AGGATCCGGGCGGGCTCGTCGCGGT) (SEQ ID NO: 29) were made to amplify the upstream region of the aIIK gene containing an internal BamHI restriction site, and aIIK-F2 (TGGATCCGGCGCGTATCGCCAACCGCTAC) (SEQ ID NO: 30) with a BamHI and aIIK-R2 (AAAGCTTCCCGGTAGTTCGCCATATGTGACCCG) (SEQ ID NO: 31) with a HindIII restriction site were made to amplify the downstream region of the aIIK gene. Between the internal BamHI restriction site and aIIK-F2, a 1698 bp (566 amino acid) gap was generated for the deletion of almost entire 2388 bp aIIK gene. When the two overlapping fragments are combined at BamHI restriction site, the reading frame is preserved, which allows for deletion of the target aIIK gene with a minimum impact on the downstream genes.

    • b) PCR amplification of DNA fragments: S. tsukubaensis genomic DNA obtained in Example 2 was PCR amplified using a Biorad iCycler Thermal Cycler using the same conditions as described in the paragraph ii of Example 4b, using aIIK-F1+aIIK-R1 and aIIK-F2+aIIK-R2 primer combinations. The PCR-amplified products were cloned into a pUC19 cloning vector, and the sequence analysis of cloned PCR products confirmed their respective DNA sequence.
    • c) Construction of a temperature-sensitive pKC1139-based and suicide pKC1132-based vectors to be used in the disruption of the S. tsukubaensis aIIK gene by homologous recombination: The F1-R1 and F2-R2 amplified fragments of the flanking regions of the aIIK gene were excised from pUC19 by restriction enzymes EcoRI and BamHI and HindII and BamHI, respectively. Vectors pKC1139 and pKC1132 were previously cut with EcoRI and HindIII restriction enzymes, and the two fragments were combined and ligated into each of the target vector, making pKC1139-aIIK and pKC1132-aIIK, respectively.
    • d) Introduction of vector for in-frame disruption of the aIIK gene into the S. tsukubaensis NRRL 18488 strain: Plasmid construct pKC1139-aIIK was introduced into S. tsukubaensis NRRL 18488 strain by the same conjugation procedure as described in Example 4d.
    • e) Selection for stable secondary recombinant strains of S. tsukubaensis with disrupted aIIK gene: S. tsukubaensis exconjugants of vector pKC1139-aIIK, grown at 28° C. on Sporulation medium with addition of 50 μg/ml apramycin were inoculated into liquid TSB medium and grown in shake flasks at 28° C. and 210 rpm with the addition of 50 μg/ml apramycin to produce good seed culture. After 24 h, seed culture was subcultivated into a new shake flask with fresh TSB medium with the addition of 50 μg/ml apramycin and grown at an increased temperature, higher than 34° C., and 210 rpm. Above 34° C. the pKC1139-based vector is unable to replicate and is forced to integrate into the S. tsukubaensis genome, thus yielding primary recombinants. The culture was then subcultivated several times into new shake flasks with fresh TSB medium without apramycin, allowing the pKC1139-based vector to be removed by homologous recombination, then plated onto the Sporulation medium and grown at 28° C. Harvested spores were filtered and serial dilution was made on plates of Sporulation medium. After 5-8 days, single colonies were patched onto plates with Sporulation medium, and on plates of Sporulation medium with apramycin. Primary recombinants are still resistant to apramycin, while secondary recombinants lost the apramycin resistance and cannot grow on Sporulation medium with apramycin. True secondary recombinant mutants with the desired in-frame deletion of the aIIK gene were identified against wild type revertants using Southern hybridization as described in Example 4f.
    • f) Fermentative tacrolimus production of aIIK disrupted mutants derived by secondary homologous recombination using pKC1139-aIIK: Tacrolimus production for aIIK disrupted mutants was performed as described in example 4g with no antibiotic added to growth media.
    • g) Fermentative tacrolimus production with aIIK disrupted mutants: Tacrolimus production aIIK disrupted mutants was carried out as described in example 4g. For the feeding experiments, allymalonyl-CoA and ethylmalonyl-CoA precursors, allylmalonyl-SNAC, allylmalonyl-diSNAC and ethylmalonyl-SNAC, were added to the Fermentation medium at 5-20 mM concentration.
    • h) Determination of tacrolimus and ascomycin production with HPLC of aIIK disrupted mutants derived by secondary recombination using pKC1139-aIIK: For the determination of tacrolimus and ascomycin production of aIIK disrupted mutants the same method was used as described in Example 4h.

Tacrolimus Ascomycin Dihydrotacrolimus production production production Description of strain (mg/l) (mg/l) (mg/l) NRRL 18488 (w.t.) 36.8 ± 4.3  3.4 ± 0.6 <1.0 ΔallKa 0.0 3.7 ± 0.5 0.0 ΔallKa + 8.3 ± 2.2 2.2 ± 0.6 0.0 allylmalonyl-SNAC ΔallKa + 7.1 ± 2.1 3.8 ± 0.5 0.0 allylmalonyl-diSNAC ΔallKa + 0.0 11.8 ± 2.6  0.0 ethylmalonyl-SNAC aSecondary recombinant mutants with disrupted allK gene. Mutants derived by secondary homologous recombination using pKC1139-allK.

Isolated secondary recombinant mutants with disrupted aIIK gene caused complete abolishment of tacrolimus and dihydrotacrolimus production. When allylmalonyl-SNAC or allylmalonyl-diSNAC were added to the Fermentation medium, production of tacroliomus was re-established. Similarly, when ethylmalonyl-SNAC was added, ascomycin production was substantially increased.

Example 7 Construction of Vectors for Overexpression of the AIIP Gene, Construction of Mutant Strains of S. tsukubaensis NRRL 18488 with Overexpressed AIIP and Analysis of Tacrolimus and Ascomycin Production of the Said Mutants

    • a) Chemical synthesis of the AIIP gene: The DNA sequence of the genome of S. tsukubaensis NRRL 18488, based on a 454-whole genome sequencing was used to design and synthesize the DNA sequence of the AIIP gene conferring NdeI restriction site at the 5′-end of the ORF and Xba I restriction site at the 3′-end of the ORF.
    • b) Construction of a pSET152-based expression vector for overexpression of the AIIP gene: The synthesized AIIP gene was cut by restriction enzymes NdeI and XbaI. Erm* promoter sequence was previously introduced into the multiple cloning site of the pSET152 vector using EcoRI and XbaI restriction sites generating a NdeI site to the 3′-end of the promoter sequence. This vector was cut with NdeI and XbaI and ligated with the NdeI and XbaI fragment of the AIIP gene to generated pSET-152-AIIP plasmid.
    • c) Overexpression of the AIIP gene into the S. tsukubaensis NRRL 18488 strain:
      • Plasmid construct pSET152-AIIP was introduced into S. tsukubaensis NRRL 18488 strain by conjugation procedure as described in Example 4d.
    • d) Determination of tacrolimus and ascomycin production of S. tsukubaensis mutants conferring pSET152-AIIP plasmid.

For the determination of tacrolimus and ascomycin production HPLC method was used as described in Example 4h.

% of ascomycin Tacrolimus production compared to Description of strain production (mg/l) tacrolimus production NRRL 18488 (w.t.) 31.2 ± 14.6 12.7 ± 3.0 Strains with overexpressed 39.3 ± 12.0 12.1 ± 3.2 AllP gene

Isolated recombinant mutants with in which AIIP gene was over expressed showed 25% increased tacrolimus production compared to the wild type strain Streptomyces tsukubaensis NRRL 18488.

Example 8 Construction of Vectors for Over Expression of the Ecm Gene, Construction of Mutant Strains of S. tsukubaensis NRRL 18488 with Ecm Gene Over Expressed and Analysis of Tacrolimus and Ascomycin Production of the Said Mutants

    • a) Chemical synthesis of the ecm gene: The DNA sequence of the genome of S. tsukubaensis NRRL 18488, based on a 454-whole genome sequencing was used to design and chemically synthesize the DNA sequence of the ecm gene conferring NdeI restriction site at the 5′-end of the ORF and XbaI restriction site at the 3′-end of the ORF.
    • b) Construction of a pSET152-based expression vector for over expression of the AIIP gene: The synthesized ecm gene fragment was cut by restriction enzymes NdeI and XbaI. Erm* promoter sequence was previously introduced into the multiple cloning site of the pSET152 vector using EcoRI and XbaI restriction sites adding a NdeI site to the 3′-end of the promoter sequence. This vector was cut with NdeI and XbaI and ligated with the NdeI and XbaI fragment of the AIIP gene to generate pSET-152-ecm construct.
    • c) Introduction of vector for over expression of the ecm gene into the S. tsukubaensis NRRL 18488 strain:
      • Plasmid construct pSET152-ecm was introduced into S. tsukubaensis NRRL 18488 strain by conjugation procedure as described in Example 4d.
    • d) HPLC analysis of tacrolimus and ascomycin production in ecm over expressing mutants

For the determination of tacrolimus and ascomycin production of ecm over expressing mutants method was used as is described in Example 4h.

% of ascomycin Tacrolimus production compared to Description of strain production (mg/l) tacrolimus production NRRL 18488 (w.t.) 31.6 ± 11.7 9.3 ± 2.8 Strains with overexpressed 31.4 ± 8.5  7.5 ± 2.6 ecm gene

Isolated recombinant mutants with over expressed ecm gene showed 20% reduced ascomycin production compared to the wild type strain Streptomyces tsukubaensis NRRL 18488.

Example 9 Construction of a Vector for Overexpression of aIIA and aIIK Genes, Complementation of aIIK-Inactivated Strains of S. tsukubaensis NRRL 18488 with this Vector and Analysis of Tacrolimus and Ascomycin Production of the Said Mutants

    • a) Design of primers: As described in Example 4, a 454-based whole genome sequencing was used on the genome of S. tsukubaensis, which allowed us to design primers for amplification of the region of all subcluster from aIIA to aIID gene. Thus, AT-exp-F1 (ACATATGCTCGGGTCGTTCGTTACGGGGAG) (SEQ ID NO: 32) with a NdeI restriction site and AT-exp-R1 (ATCTAGAACGTGGGTCATCGGCTGGTCCTTG) (SEQ ID NO: 33) with an XbaI restriction site were made to amplify these two ORFs (aIIA and aIIK).
    • b) PCR amplification of DNA fragments: S. tsukubaensis genomic DNA obtained in Example 2 was PCR amplified using a Biorad iCycler Thermal Cycler. The PCR reaction was carried out with Phusion polymerase (Finnzymes) and the buffer provided by the manufacturer in the presence of 200 μM dNTP, 3% DMSO, 0.5 μM of each primer, approximately 50 ng of template S. tsukubaensis genomic DNA and 2.5 units of enzyme in a final volume of 50 μl for 30 cycles. The thermal profile of the first 5 cycles was 98° C. for 15 sec (denaturation step), 65° C. for 30 sec (annealing step), and 72° C. for 3 min 15 sec (extension step). The thermal profile of the remaining 25 cycles was 98° C. for 15 sec (denaturation step), 60° C. for 30 sec (annealing step), and 72° C. for 3 min 15 s (extension step). The PCR-amplified product was cloned into a pUC19 cloning vector. The sequence analysis of the cloned PCR product confirmed the sequence of aIIA and al/K genes.
    • c) Construction of a pSET152-based expression vector for overexpression of aIIA and al/K genes: The 3.9 kb insert was cut from pUC19 vector by restriction enzymes NdeI and XbaI. ErmE* promoter sequence was previously introduced into the multiple cloning site of the pSET152 vector using EcoRI and XbaI restriction sites generating a NdeI site to the 3′-end of the promoter sequence. This vector was cut with NdeI and XbaI and subsequently ligated with the NdeI and XbaI fragment containing aIIA and al/K genes to generate pSET152-ermE*-aIIA-K plasmid.
    • d) Introduction of the aIIA and aIIK gene into the S. tsukubaensis strain with inactivated aliK gene, obtained in Example 6: plasmid construct pSET152-ermE*-aIIA-K was introduced into the aIIK-inactivated strain of S. tsukubaensis NRRL 18488 by conjugation procedure as described in Example 4d.
    • e) Fermentative tacrolimus production of aIIK disrupted mutants transformed with a pSET152-ermE*-aIIA-K vector: Tacrolimus production for transformed mutants was performed as described in example 4g with no antibiotic added to growth media.
    • f) Determination of tacrolimus and ascomycin production of aIIK-inactivated S. tsukubaensis mutants conferring pSET152-ermE*-aIIA-K plasmid

Tacrolimus Ascomycin Description of strain production (mg/l) production (mg/l) NRRL 18488 (w.t.) 37.7 ± 19.3 3.4 ± 1.8 ΔallK 0.0 2.6 ± 1.1 ΔallK strains with overexpressed 24.7 ± 14.1 3.4 ± 1.6 allA and allK genes

Isolated recombinant mutants of aIIK-inactivated strains in which the loss of aIIK gene activity was complemented by overexpression of aIIA and aIIK showed restored production of tacrolimus.

Example 10 Construction of a Vector for Overexpression of aIIA, aIIK, aIIR, aIID Genes, Complementation of aIIR-Inactivated Strains of S. tsukubaensis NRRL 18488 with this Vector and Analysis of Tacrolimus and Ascomycin Production of the Said Mutants

    • a) Design of primers: As described in Example 4, a 454-based whole genome sequencing was used on the genome of S. tsukubaensis, which allowed us to design primers for amplification of the region of all subcluster from aIIA to aIID gene Thus, AT-exp-F1 (ACATATGCTCGGGTCGTTCGTTACGGGGAG) (SEQ ID NO: 32) with a NdeI restriction site and AT-exp-R2 (ATCTAGAACATGCCCTAGGTACGTTTCGCGG) (SEQ ID NO: 34) with an XbaI restriction site were made to amplify these four ORFs (aIIA, aIIK, aIIR, and aIID).
    • b) PCR amplification of DNA fragments: S. tsukubaensis genomic DNA obtained in Example 2 was PCR amplified using a Biorad iCycler Thermal Cycler. The PCR reaction was carried out with Phusion polymerase (Finnzymes) and the buffer provided by the manufacturer in the presence of 200 μM dNTP, 3% DMSO, 0.5 μM of each primer, approximately 50 ng of template S. tsukubaensis genomic DNA and 2.5 units of enzyme in a final volume of 50 μl for 30 cycles. The thermal profile of the first 5 cycles was 98° C. for 15 sec (denaturation step), 65° C. for 30 sec (annealing step), and 72° C. for 3 min 15 sec (extension step). The thermal profile of the remaining 25 cycles was 98° C. for 15 sec (denaturation step), 60° C. for 30 sec (annealing step), and 72° C. for 3 min 15 sec (extension step). The PCR-amplified product was cloned into a pUC19 cloning vector. The sequence analysis of the cloned PCR product confirmed the sequence of aIIA, aIIK, aIIR and aIID genes.
    • c) Construction of a pSET152-based expression vector for overexpression of aIIA, aIIK, aIIR and aIID genes: The 6.4 kb insert was cut from pUC19 vector by restriction enzymes NdeI and XbaI. ErmE* promoter sequence was previously introduced into the multiple cloning site of the pSET152 vector using EcoRI and XbaI restriction sites generating a NdeI site to the 3′-end of the promoter sequence. This vector was cut with NdeI and XbaI and subsequently ligated with the NdeI and XbaI fragment containing aIIA, aIIK, aIIR and aIID genes to generate pSET152-ermE*-aIIA-D plasmid.
    • d) Introduction of the aIIA, aIIK, aIIR and aIID gene into the S. tsukubaensis strain with inactivated aIIR gene, obtained in Example 5: plasmid construct pSET152-ermE*-aIIA-D was introduced into the al/R-inactivated strain of S. tsukubaensis NRRL 18488 by conjugation procedure as described in Example 4d.
    • e) Fermentative tacrolimus production of aIIR inactivated mutants transformed with a pSET152-ermE*-aIIA-D vector: Tacrolimus production for transformed mutants was performed as described in example 4g with no antibiotic added to growth media.
    • f) Determination of tacrolimus and ascomycin production of aIIR-inactivated S. tsukubaensis mutants conferring pSET152-ermE*-aIIA-D plasmid

Tacrolimus Ascomycin Description of strain production (mg/l) production (mg/l) NRRL 18488 (w.t.) 36.1 ± 20.2 4.4 ± 1.5 ΔallR Era 0.0 0.0 ΔallR Era strains with 15.2 ± 7.7  3.0 ± 1.0 overexpressed allA, allK, allR and allD genes

Isolated recombinant mutants of aIIR-inactivated strains in which the loss of aIIR gene activity was complemented by overexpression of aIIA, aIIK, aIIR and aIID showed restored production of tacrolimus and ascomycin.

Example 11 Introduction of the Plasmid pSET152-ermE*-aIIA-D into the Strain Streptomyces hygroscopicus Var. Ascomyceticus ATCC14891, Overexpression of aIIA, aIIK, aIIR and aIID Genes in this Strain and Analysis of Tacrolimus and Ascomycin Production of the Said Mutants

    • a) Construction of a pSET152-based expression vector for overexpression of aIIA, aIIK, aIIR and aIID genes: pSET152-ermE*-aIIA-D plasmid was prepared as described in Example 10.
    • b) Introduction of the aIIA, aIIK, aIIR and aIID genes into the strain Streptomyces hygroscopicus var. ascomyceticus ATCC14891: Plasmid construct pSET152-ermE*-aIIA-D was introduced by transformation into electrocompetent E. coli strain ET12567 containing the conjugative plasmid pUZ8002 (Paget et al., 1999 J. Bacteriol. 181: 204-211). The plasmid pUZ8002 contains all the necessary genes for construction of conjugative pilli, however it lacks the origin of transfer and, thus, remains in the host cell (Jones et al., 1997 Mol. Microbiol. 23:169-178). Conjugation procedure of Streptomyces hygroscopicus var. ascomyceticus ATCC14891 was done as described in Kieser et al., 2000 (Practical Streptomyces genetics, A laboratory Manual. ISBN0-7084-0623-8). Exconjugants were grown at 28° C. on Sporulation medium which is described in Example 1 with addition of 50 μg/ml apramycin.
    • c) Fermentative ascomycin and tacrolimus production of strains transformed with a pSET152-ermE*-aIIA-D vector: Fermentation process for ascomycin and tacrolimus production of transformed mutants was performed as described in example 4g with no antibiotic added to growth media.
    • d) Determination of tacrolimus and ascomycin production with LC-MS/MS of Streptomyces hygroscopicus var. ascomyceticus ATCC14891 mutants overexpressing the aIIA, aIIK, aIIR and aIID genes:

Sample preparation: To 5 ml of well shaken broth 5 ml of methanol was added and samples were placed on a shaker for 1 hour to extract samples. After extraction, 1 ml of methanol extract of broth was taken to 1.5 ml tube and centrifuged for 10 min at 14000 rpm. 0.8 ml of supernatant was transferred into vials and to perform LC-MS/MS analysis.

Method for tacrolimus and ascomycin determination: Identity of FK506 and FK520 in cultivation broths was determined by LC-MS/MS analysis. We used the Agilent 1100 series LC-MS system coupled with Watters Micromass Quattro micro detector using reversed phase column (Gemini C18 column, 5 μm, 150 mm×2 mm i.d.) from Phenomenex. The separation was performed at a flow rate of 0.250 ml/min by gradient elution with 0.5% TFA as solvent A and acetonitrile as solvent B. The gradient program was: 60% A, 0 min; 60-20% A, 0-17 min; 20-60% A, 17-18 min; 60% A, 18-30 min and the injection volume 10 μL at temperature of the column 45° C. was used. The mass selective detector (Waters, Quattro micro API) was equipped with an electrospray ionisation using a cone voltage of 20 V and capillary voltage of 3.5 kV for positive ionization of the analytes. Dry nitrogen was heated to 350° C., the drying gas flow was 400 l/h and collision energy was 20 eV. In ESI+ positive mode, an ion of m/z=826.5 that corresponds to a capture of a sodium ion of FK506 ([M+Na]+) was most intensive, in accordance with the results of other investigators (see Yuan J. et al. 2008, J. Chromatogr., B: Anal. Technol. Biomed Life Sci. 868, 34-41). For FK506 identity confirmation, multiple reaction-monitoring mode was used and the transition FK506 m/z 826.5 [M+Na]+→m/z 616.4 was recorded. Analogously, for FK520 monitoring the transition m/z 814.5 [M+Na]+→m/z 604.4 was recorded. Tacrolimus was eluted at approx. 18.2 min and ascomycin at approx. 17.5-17.7 min. Abundance of FK506 and FK520 could not be determined therefore only presence or absence of both compounds could be established (FIG. 2).

Tacrolimus Ascomycin Description of strain production production ATCC 18491 (w.t.) absent present Strains with overexpressed present present allA, allK, allR and allD genes

Isolated recombinant mutants of Streptomyces hygroscopicus var. ascomyceticus ATCC14891 in which aIIA, aIIK, aIIR and aIID genes were overexpressed showed production of tacrolimus in addition to ascomycin which is usually produced by this strain.

Example 12 Construction of Vectors for Deletion of a Large Part of the all Subcluster (from aIID to aIIS), Construction of Mutant Strains of S. tsukubaensis NRRL 18488 with this Part of the all Subcluster Deleted and Analysis of Tacrolimus and Ascomycin Production of the Said Mutants

    • a) Design of primers: As described in Example 4, a 454-based whole genome sequencing was used on the genome of S. tsukubaensis, which allowed us to design primers for amplification of the regions flanking the region between aIID and aIIS genes, based on a known DNA sequence of the region upstream of the aIID gene and downstream of the aIIS gene. Thus, KS-delF2b (TGGATCCGGCGCGTATCGCCAACCGCTAC) (SEQ ID NO: 30) with a BamHI restriction site and AIIRexpR1 (ATCTAGAGGCGTTCGGATTCGCTCACCG) (SEQ ID NO: IQ with an XbaI restriction site were made to amplify the region upstream of the aIID gene, and ClusDelF2 (ATCTAGAGGGCGGATACGTCACCGGCG) (SEQ ID NO: 36) with an XbaI and ClusDelR2b (CCAAGCTTATGGAGATCATCGAAGGCAGC) (SEQ ID NO: 37) with an HindIII restriction site were made to amplify the region downstream of the aIIS gene. Between primers AIIRexpR1 and ClusDelF2, a 6262 bp gap was generated for the deletion of aIID, aIIM, aIIN, aIIP, aIIO and aIIS genes.
    • b) PCR amplification of DNA fragments: S. tsukubaensis genomic DNA obtained in Example 2 was PCR amplified using a Biorad iCycler Thermal Cycler. The PCR reaction was carried out with Phusion polymerase (Finnzymes) and the buffer provided by the manufacturer in the presence of 200 μM dNTP, 3% DMSO, 0.5 μM of each primer, approximately 50 ng of template S. tsukubaensis genomic DNA and 2.5 units of enzyme in a final volume of 50 μl for 30 cycles. The thermal profile of the first 5 cycles was 98° C. for 15 sec (denaturation step), 65° C. for 30 sec (annealing step), and 72° C. for 1 min (extension step). The thermal profile of the remaining 25 cycles was 98° C. for 15 sec (denaturation step), 60° C. for 30 sec (annealing step), and 72° C. for 1 min (extension step). The PCR-amplified products were cloned into a pUC19 cloning vector. The sequence analysis of the cloned PCR product confirmed the sequence of the amplified upstream and downstream regions.
    • c) Construction of a temperature-sensitive pKC1139-based vector to be used in the disruption of the aIID-aIIS region of the S. tsukubaensis genome by homologous recombination: The KS-delF2b-AIIRexpR1 and ClusDelF2-ClusDelR2 amplified fragments of the flanking regions were excised from pUC19 by restriction enzymes BamHI and XbaI and XbaI and HindIII, respectively. Vector pKC1139 was previously cut with BamHI and HindIII restriction enzymes, and the two fragments were combined and ligated into the target vector, making pKC1139-ClusDel.
    • d) Introduction of vector for deletion of the aIID-aIIS region of all subcluster into the S. tsukubaensis NRRL 18488 strain: Plasmid construct pKC1139-ClusDel was introduced into S. tsukubaensis NRRL 18488 strain by the same conjugation procedure as described in Example 4d.
    • e) Selection for stable secondary recombinant strains of S. tsukubaensis with deleted aIID-aIIS region: Selection of secondary recombinants was carried out using the same procedure as described in Example 6d.
    • f) Fermentative tacrolimus production of mutants with deleted aIID-aIIS region, derived by secondary homologous recombination using pKC1139-ClusDel: Fermentation process for tacrolimus production of the aIID-aIIS-deleted mutants was performed as described in example 4g with no antibiotic added to growth media.
    • g) Determination of tacrolimus and ascomycin production with HPLC of aIID-aIIS deleted mutants derived by secondary recombination using pKC1139-ClusDel: For the determination of tacrolimus and ascomycin production of aIID-aIIS-deleted mutants the same method was used as described in Example 4h.

Tacrolimus Ascomycin Description of strain production (mg/l) production (mg/l) NRRL 18488 (w.t.) 37.7 ± 19.3 3.4 ± 1.8 ΔallD-allSa 0.0 0.0 aSecondary recombinant mutants with deleted allD-allS region. Mutants derived by secondary homologous recombination using pKC1139-ClusDel.

Isolated secondary recombinant mutants with disrupted aIID-aIIS region caused complete abolishment of tacrolimus and ascomycin production.

Claims

1. A genetically modified strain of a microorganism belonging to the genus Streptomyces, wherein said microorganism comprises genes represented by SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO:8, SEQ ID NO: 9 and SEQ ID NO: 10, which are involved in the metabolism and/or the biosynthesis of ethylmalonyl-CoA and/or allylmalonyl-CoA, wherein in said genetically modified strain of said microorganism, one or more of said genes is inactivated and/or over expressed.

2. The genetically modified strain of a microorganism according to claim 1, wherein said strain has a native or engineered polyketide synthase activity.

3. A process for the preparation of tacrolimus, wherein the process comprises the step of cultivating the genetically modified strain of claim 1.

4. The process according to claim 3, wherein the process is carried out under the external addition of allylmalonyl-CoA and/or at least one precursor of allylmalonyl-CoA.

5. A Streptomyces tsukubaensis strain deposited at Deutsche Sammlung von Microorganismen and Zellkulturen GmbH (Braunschweig, Germany) and having a deposit number selected from the group consisting of DSM 22507, DSM 22509, DSM22511, DSM 22506 and DSM 22510.

Referenced Cited
Foreign Patent Documents
WO 00/20601 April 2000 WO
WO 03/070908 August 2003 WO
WO 2006/011156 February 2006 WO
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Patent History
Patent number: 8980585
Type: Grant
Filed: Jul 9, 2010
Date of Patent: Mar 17, 2015
Patent Publication Number: 20120295316
Assignee: Lek Pharmaceuticals D.D. (Ljubljana)
Inventors: Hrvoje Petkovic (Ljubljana), Enej Kuscer (Ljubljana), Stefan Fujs (Ljubljana), Gregor Kopitar (Ljubljana), Peter Mrak (Ljubljana), Gregor Kosec (Ljubljana)
Primary Examiner: Tekchand Saidha
Application Number: 13/383,182
Classifications
Current U.S. Class: Containing Two Or More Hetero Rings (435/118); Transformants (e.g., Recombinant Dna Or Vector Or Foreign Or Exogenous Gene Containing, Fused Bacteria, Etc.) (435/252.3)
International Classification: C12P 17/16 (20060101); C12N 1/20 (20060101); C12N 15/52 (20060101); C12P 17/18 (20060101);